Systems and methods for predicting therapeutic sensitivity

ABSTRACT

Methods, systems, and software are provided for using organoid cultures, e.g., patient-derived tumor organoid cultures, to improve treatment predictions and outcomes.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No. 62/924,621, filed on Oct. 22, 2019, and U.S. Provisional Application No. 62/944,292, filed on Dec. 5, 2019, which are expressly incorporated by reference in their entireties for all purposes.

TECHNICAL FIELD

The present disclosure relates generally to use of organoids for predicting patient sensitivity to therapeutic agents.

BACKGROUND

Precision oncology is the practice of tailoring cancer therapy to the unique genomic, epigenetic, and/or transcriptomic profile of an individual tumor. This is in contrast to conventional methods for treating a cancer patient based merely on the type of cancer the patient is afflicted with, e.g., treating all breast cancer patients with a first therapy and all lung cancer patients with a second therapy. Precision oncology was borne out of many observations that different patients diagnosed with the same type of cancer, e.g., breast cancer, responded very differently to common treatment regimes. Over time, researchers have identified genomic, epigenetic, and transcriptomic markers that facilitate some level of prediction as to how an individual cancer will respond to a particular treatment modality.

Therapy targeted to specific genomic alterations is already the standard of care in several tumor types (e.g., as suggested in the National Comprehensive Cancer Network (NCCN) guidelines for melanoma, colorectal cancer, and non-small cell lung cancer). These few, well known mutations in the NCCN guidelines can be addressed with individual assays or small next generation sequencing (NGS) panels. However, for the largest number of patients to benefit from personalized oncology, molecular alterations that can be targeted with off-label drug indications, combination therapy, or tissue agnostic immunotherapy should be assessed. See Schwaederle et al. 2016 JAMA Oncol. 2, 1452-1459; Schwaederle et al. 2015 J Clin Oncol. 32, 3817-3825; and Wheler et al. 2016 Cancer Res. 76, 3690-3701. Large panel NGS assays also cast a wider net for clinical trial enrollment. See Coyne et al. 2017 Curr. Probl. Cancer 41, 182-193; and Markman 2017 Oncology 31, 158,168.

Genomic analysis of tumors is rapidly becoming routine clinical practice to provide tailored patient treatments and improve outcomes. See Fernandes et al. 2017 Clinics 72, 588-594. Indeed, recent studies indicate that clinical care is guided by NGS assay results for 30-40% of patients receiving such testing. See Hirshfield et al. 2016 Oncologist 21, 1315-1325; Groisberg et al. 2017 Oncotarget 8, 39254-39267; Ross et al. JAMA Oncol. 1, 40-49; and Ross et al. 2015 Arch. Pathol. Lab Med. 139, 642-649. There is growing evidence that patients who receive therapeutic advice guided by genetics have better outcomes. See, for example Wheler et al. who used matching scores (e.g., scores based on the number of therapeutic associations and genomic aberrations per patient) to demonstrate that patients with higher matching scores have a greater frequency of stable disease, longer time to treatment failure, and greater overall survival (2016 Cancer Res. 76, 3690-3701). Such methods may be particularly useful for patients who have already failed multiple lines of therapy.

Targeted therapies have shown significant improvements in patient outcomes, especially in terms of progression-free survival. See Radovich et al. 2016 Oncotarget 7, 56491-56500. Further, recent evidence reported from the IMPACT trial, which involved genetic testing of advanced stage tumors from 3,743 patients and where approximately 19% of patients received matched targeted therapies based on their tumor biology, showed a response rate of 16.2% in patients with matched treatments versus 5.2% in patients with non-matched treatments. See Bankhead. “IMPACT Trial: Support for Targeted Cancer Tx Approaches.” MedPageToday. Jun. 5, 2018. The IMPACT study further found that the three-year overall survival for patients given a molecularly matched therapy was more than twice that of non-matched patients (15% vs. 7%). See Id. and ASCO Post. “2018 ASCO: IMPACT Trial Matches Treatment to Genetic Changes in the Tumor to Improve Survival Across Multiple Cancer conditions.” The ASCO POST. Jun. 6, 2018. Estimates of the proportion of patients for whom genetic testing changes the trajectory of their care vary widely, from approximately 10% to more than 50%. See Fernandes et al. 2017 Clinics 72, 588-594.

One example of a genomic trait that has been linked to the efficacy of particular therapies are mutations in the BRCA1, BRCA2, or PALB2 homologous recombination genes. A class of pharmacological inhibitors of Poly ADP ribose polymerase 1 (PARP1), known as PARP inhibitors (PARPi), have therapeutic efficacy for treating some cancers containing a mutation in the BRCA1, BRCA2, or PALB2 homologous recombination genes. PARP1 is an essential enzyme in the error-prone microhomology-mediated end joining (MMEJ) DNA repair pathway. Sharma S. et al., Cell Death Dis. 6(3):e1697 (2015). In the absence of PARP1 activity, DNA replication forks stall when encountering a single-strand break. Fork stalling ultimately results in double-stranded chromosomal breaks that can be repaired by homologous recombination (HR) repair, which is much less error prone than the MMEJ pathway.

Unlike other DNA repair proteins, which are commonly deficient in cancer cells, PARP1 has been shown to be over-expressed in certain cancer types. It has been theorized that increased MMEJ DNA repair, relative to homologous repair, results in the accumulation of genomic mutations, which can lead to the development of cancer. However, the efficacy of PARP inhibitors is not completely understood. For instance, not all cancers with a BRCA1, BRCA2, or PALB2 mutation are sensitive to PARP inhibitors. Further, some cancers without a mutation in any homologous recombination protein are sensitive to PARP inhibitors.

SUMMARY

Given the above background, what is needed in the art are improved ways to identify which cancer patients will respond favorably to PARP inhibitors. The present disclosure addresses these and other needs by providing systems and methods for using organoid cultures to improve treatment predictions and outcomes. There is also a need for systems and methods for assessing the effectiveness of various drugs on one or more tumor organoid lines. Such systems or methods may be used to determine if a specific drug may be useful in killing cancer cells with specific genetic mutations or phenotypes.

Also provided herein is a high-throughput drug screening method and system more applicable for the unique characteristics of tumor organoids (TOs). The systems and methods provided herein are capable of measuring TO therapeutic response with high statistical confidence and exquisite inter-assay reproducibility. This approach can be utilized in research settings to elucidate heterogeneity of therapeutic responses within and among patients, and may be utilized in the clinical laboratory to potentially guide precision oncology treatments. In some embodiments, the platform couples high content fluorescent confocal imaging analysis with a robust statistical analytical approach to measure hundreds of discrete data points of TO viability from as few as 1×10³ cells. This approach was validated through evaluating responses to hundreds of small molecule inhibitors as well as a panel of chemotherapeutic agents in TO models derived from different patients.

Additional aspects and advantages of the present disclosure will become readily apparent to those skilled in this art from the following detailed description, wherein only illustrative embodiments of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different embodiments, and its several details are capable of modifications in various obvious respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a block diagram of an example of a computing device for using information derived from organoid-based assays to improve therapeutic outcomes, in accordance with some embodiments of the present disclosure.

FIG. 2 illustrates an example of a distributed diagnostic environment for evaluating therapeutic regimes using information derived from tumor organoid studies, in accordance with some embodiments of the present disclosure.

FIGS. 3A, 3B, 3C, and 3D illustrate dose response curves for the treatment of four patient-derived tumor organoid cell lines with olaparib, in accordance with some embodiments of the present disclosure.

FIGS. 4A and 4B collectively show example image of high-content fluorescent confocal imaging analysis using the subject methods described herein. (Top panels) Brightfield (top left), Hoechst 33342 (top right), Caspase 3/7 (bottom left), and TO-PRO-3 (bottom right) staining is shown for vehicle control (FIG. 4A) and staurosporine treated (FIG. 4B) gastric cancer TOs. (Bottom panels) Overlays of the fluorescent channels and the result of image analysis are shown side by side. The outline of the larger objects in the right panels indicates the area of a given TO. Live and dead cells are shown in the image analysis panels. Scale bars represent 100 microns.

FIGS. 5A and 5B illustrate examples of dose-response curves determined from carbocyanine monomer nucleic acid staining (TO-PRO-3; FIG. 5A) and caspase 3/7 staining (Caspase 3/7; FIG. 5B), in accordance with some embodiments of the present disclosure.

FIG. 6 shows a summary of a study, showing that a classifier trained using data sets obtained from the subject methods is capable of predicting morphological responses to pharmacological agents in a tumor organoid sample based on a brightfield image of the sample, in accordance with some embodiments of the present disclosure.

FIGS. 7A and 7B collectively illustrate a neural network-based model for predicting TO drug response. FIG. 7A shows brighfield, real fluorescence, and generated fluorescence images for colon, lung, ovarian, and breast cancers. FIG. 7B illustrates the correlation between the neural network predictions and fluorescent-based drug responses for the colon, lung, ovarian, and breast cancers.

FIG. 8 illustrates AUC ROC curves between caspase and generated viabilities for the PARPi drug screen described in Example 5.

FIGS. 9A and 9B illustrate viability data for a tumor organoid having a low HRD score, a pathogenic BRCA1 mutation, no BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 10A and 10B illustrate viability data for a colorectal tumor organoid having a high HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 11A and 11B illustrate viability data for a tumor organoid having a low HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 12A and 12B illustrate viability data for a tumor organoid having a low HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 13A and 13B illustrate viability data for a tumor organoid having a high HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 14A and 14B illustrate viability data for a tumor organoid having a low HRD score, no BRCA1 or BRCA2 mutations, BRCA1 LOH, and no BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 15A and 15B illustrate viability data for a tumor organoid having a high HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control). Lower doses of PARPi were more effective for this organoid than the low HRD shown in the previous figures organoid.

FIGS. 16A and 16B illustrate viability data for a tumor organoid having a low HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 17A and 17B illustrate viability data for a tumor organoid having a high HRD score, no BRCA1 or BRCA2 mutations, no BRCA1 LOH and having BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 18A and 18B illustrate viability data for a tumor organoid having a low HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

Like reference numerals refer to corresponding parts throughout the several views of the drawings.

DETAILED DESCRIPTION

In some embodiments, the present disclosure provides systems and methods for using organoid cultures, e.g., patient-derived tumor organoid cultures, to improve treatment predictions and outcomes.

For instance, in one aspect, the disclosure provides methods and systems for performing methods of training a classifier to discriminate between two or more tumor sensitivities to a poly ADP ribose polymerase (PARP) inhibitor. In some embodiments, the method includes obtaining a data set comprising, for each respective tissue sample in a plurality of tissue samples, (i) a corresponding plurality of nucleic acid features of the tissue sample, and (ii) a corresponding indication of the sensitivity of a respective organoid cultured from one or more cells of the tissue sample to the PARP inhibitor. The method then includes training an untrained classifier against at least (i) the corresponding plurality of features and (ii) the corresponding indication of the sensitivity of the organoid to the PARP inhibitor, across the plurality of tissue samples, thereby obtaining a trained classifier that discriminates between the two or more tumor sensitivities to a poly ADP ribose polymerase (PARP) inhibitor.

In another aspect, the disclosure provides method and systems for performing methods of recommending therapy for treating a cancer in a subject. In some embodiments, the method includes obtaining a first test data set comprising a plurality of nucleic acid features of a tumor biopsy from the test subject. The method then includes evaluating the first test data set using a classifier trained to discriminate between two or more tumor sensitivities to a first poly ADP ribose polymerase (PARP) inhibitor. The classifier is trained against, for each respective training tissue sample in a plurality of training tissue samples, at least (i) the plurality of nucleic acid features obtained from the respective training tissue sample, and (ii) a corresponding indication of the sensitivity of a respective organoid cultured from one or more cells of the respective training tissue sample to the first PARP inhibitor. In some embodiments, the sensitivity of the training tissue sample is determined in a two-dimensional cell culture, a three-dimensional cell culture prepared in a matrix, a three-dimensional cell culture prepared in suspension culture, a cell culture suspension, or a xenograft model. A first tumor sensitivity in the two or more tumor sensitivities to the first PARP inhibitor is associated with a first recommendation, in a plurality of recommendations, to treat the cancer in the subject with the first PARP inhibitor. A second tumor sensitivity in the two or more tumor sensitivities to the first PARP inhibitor is associated with a second recommendation, in the plurality of recommendations, not to treat the cancer in the subject with the first PARP inhibitor. In some embodiments, the method includes providing a respective recommendation, in the plurality of recommendations, for treating the cancer in the test subject based on the results of the evaluation.

In another aspect, the disclosure provides methods and systems for performing methods of treating, or assigning therapy for, a BRCA1-/BRCA2-cancer in a test subject. In some embodiments, the methods include determining a probability or likelihood that the cancer will be sensitive to a poly ADP ribose polymerase (PARP) inhibitor, and treating cancer in the subject. When the probability or likelihood that the cancer will be sensitive to the PARP inhibitor satisfies a sensitivity threshold, the method includes administering, or communicating, a recommended therapy comprising the PARP inhibitor to the test subject. When the probability or likelihood that the cancer will be sensitive to the PARP inhibitor does not satisfy a sensitivity threshold, the method includes administering, or communicating, a recommended therapy that does not include the PARP inhibitor to the test subject.

In another aspect, the disclosure provides methods and systems for performing methods of treating a cancer other than breast cancer or ovarian cancer in a test subject. In some embodiments, the methods include determining a probability or likelihood that the cancer will be sensitive to a poly ADP ribose polymerase (PARP) inhibitor, and treating cancer in the subject. When the probability or likelihood that the cancer will be sensitive to the PARP inhibitor satisfies a threshold likelihood, the method includes administering, or communicating, a recommended therapy comprising the PARP inhibitor to the test subject. When the probability or likelihood that the cancer will be sensitive to the PARP inhibitor does not satisfy a threshold likelihood, the method includes administrating, or communicating, a recommended therapy that does not include the PARP inhibitor to the test subject.

In another aspect, the disclosure provides methods and systems for performing methods of providing a clinical report for a cancer patient to a physician. In some embodiments, the methods include obtaining a first test data set comprising features of a transcriptome from a tumor biopsy from the cancer patient. In some embodiments, the methods include evaluating the first test data set using a classifier trained, e.g., as described herein, to discriminate between two or more tumor sensitivities to a first poly ADP ribose polymerase (PARP) inhibitor. The methods then include receiving a recommended therapy for the cancer patient from the classifier, and including the recommended therapy, or sending the recommended therapy to a third party for inclusion, in a clinical report for the cancer patient.

In another aspect, the disclosure provides methods and systems for performing methods of identifying an inhibitor of poly ADP ribose polymerase (PARP). In some embodiments, the methods include obtaining a tissue sample that is sensitive to a known PARP inhibitor, and culturing one or more organoids, each respective organoid in the one or more organoids from one or more cells of the tissue sample. The methods then include exposing the one or more of the cultured organoids to one or more concentrations of a candidate molecule, and measuring the fitness of cells in the one or more organoids following the exposure to the one or more concentrations of the candidate molecule. A reduced fitness of cells in the one or more organoids is indicative that the candidate molecule is a PARP inhibitor.

In another aspect, the disclosure provides methods and systems for performing methods of identifying a new use for a pharmaceutical compound of a first pharmaceutical class. In some embodiments, the methods include obtaining a plurality of tissue samples, wherein each respective tissue sample in the plurality of tissue samples is sensitive to a respective class of pharmaceutical agents in a plurality of classes of pharmaceutical agents that excludes the first pharmaceutical class. The methods then includes culturing, for each respective tissue sample in the plurality of tissue samples, one or more respective organoids from one or more cells of the respective tissue sample, thereby generating a plurality of organoid cultures. The methods then include exposing, for each organoid culture in the plurality of organoid cultures, the respective one or more organoids to one or more concentrations of the pharmaceutical agent, and measuring, for each organoid culture in the plurality of organoid cultures, the fitness of cells in the respective one or more organoids following the exposure to the pharmaceutical agent. Reduced fitness of the cells in the respective one or more organoids is indicative that the pharmaceutical molecule shares pharmacological properties with the class of pharmaceutical compounds in the plurality of classes of pharmaceutical classes to which the tissue sample corresponding to the respective one or more organoids is sensitive.

In another aspect, the disclosure provides methods and systems for performing methods of determining the eligibility of a cancer patient for a clinical trial of a candidate cancer pharmaceutical agent. In some embodiments, the methods include obtaining a tumor biopsy from the cancer patient, and culturing one or more tumor organoids from one or more cells of the tumor biopsy. The methods then include exposing the one or more tumor organoids to one or more concentrations of the candidate cancer pharmaceutical agent, and measuring the fitness of cells in the one or more tumor organoids following the exposure to the one or more concentrations of the candidate cancer pharmaceutical agent. The methods then include determining whether the cancer patient is eligible for the clinical trial based on at least the measured fitness of the cells in the one or more tumor organoids, wherein reduced fitness of the cells in the one or more tumor organoids is indicative that the cancer patient is eligible for the clinical trial.

In another aspect, the disclosure provides methods and systems for performing methods of determining the eligibility of a cancer patient for a clinical trial of a candidate cancer pharmaceutical agent. In some embodiments, the methods include obtaining a first test data set comprising a plurality of nucleic acid features of a tumor biopsy from the cancer patient. The methods then include evaluating the first test data set using a classifier trained to discriminate between two or more tumor sensitivities to the candidate cancer pharmaceutical agent. The classifier is trained against, for each respective training tissue sample in a plurality of training tissue samples, at least (i) the plurality of nucleic acid features obtained from the respective training tissue sample, and (ii) a corresponding indication of the sensitivity of a respective organoid cultured from one or more cells of the respective training tissue sample to the candidate cancer pharmaceutical agent. A first tumor sensitivity in the two or more tumor sensitivities to the candidate cancer pharmaceutical agent is associated with an indication that the cancer patient is eligible for the clinical trial. A second tumor sensitivity in the two or more tumor sensitivities to the candidate cancer pharmaceutical agent is associated with an indication that the cancer patient is eligible for the clinical trial. The methods then include determining whether the cancer patient is eligible for the clinical trial based on at least the evaluation.

In another aspect, the disclosure provides methods and systems for performing methods of identifying a resistance to a chemotherapeutic agent in a patient with cancer. In some embodiments, the methods include obtaining a first test data set comprising a plurality of nucleic acid features of a tumor biopsy from the patient with cancer. The methods then include evaluating the first test data set using a classifier trained to discriminate between two or more tumor sensitivities to the chemotherapeutic agent. The classifier is trained against, for each respective training tissue sample in a plurality of training tissue samples, at least (i) the plurality of nucleic acid features obtained from the respective training tissue sample, and (ii) a corresponding indication of the sensitivity of a respective organoid cultured from one or more cells of the respective training tissue sample to the chemotherapeutic agent. A first tumor sensitivity in the two or more tumor sensitivities to the candidate cancer pharmaceutical agent is associated with an indication that the patient's cancer is resistant to the chemotherapeutic agent. A second tumor sensitivity in the two or more tumor sensitivities to the candidate cancer pharmaceutical agent is associated with an indication that the patient's cancer is not resistant to the chemotherapeutic agent. The methods then include providing a report indicating whether the patient's cancer is resistant to the chemotherapeutic agent based on at least the results of the evaluation.

In another aspect, the disclosure provides methods and systems for evaluating an effect of a cancer therapeutic agent. In some embodiments, the method includes providing a plurality of tumor organoids cultured in a tumor organoid culture medium, where the plurality of tumor organoids is divided into a plurality of tumor organoid subsets. The method then includes contacting each subset in the plurality of tumor organoid subsets with a cancer therapeutic agent. The method also includes contacting each subset in the plurality of tumor organoid subsets with one or more cell death detection agents and a total cell detection agent. The method then includes obtaining a tumor organoid profile for each subset in the plurality of subset. In some embodiments, the tumor organoid profile includes a cell viability value for every tumor organoid in the subset. The method then includes assessing the effect of the cancer therapeutic agent based on the tumor organoid profiles.

In another aspect, the disclosure provides methods and systems for assigning a treatment dosage of a cancer therapeutic agent for a subject in need thereof. In some embodiments, the method includes providing a plurality of tumor organoids cultured in a tumor organoid culture medium, where the tumor organoids are derived from a subject, and where the plurality of tumor organoids is divided into a plurality of tumor organoid subsets. The method then includes contacting each subset in the plurality of tumor organoid subsets with a different dosage of a cancer therapeutic agent. The method also includes contacting each subset in the plurality of tumor organoid subsets with one or more cell death detection agents and a total cell detection agent. The method then includes obtaining a tumor organoid profile for each subset in the plurality of subset, where the tumor organoid profile includes a cell viability value for every tumor organoid in the subset. The method then includes determining a therapeutic agent dosage curve from the tumor organoid profiles. The method then includes assigning a treatment dosage of the cancer therapeutic agent to the subject based on the therapeutic agent dosage curve.

Definitions.

The terminology used in the present disclosure is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention. As used in the description of the invention and the appended claims, the singular forms “a”, “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. It will also be understood that the term “and/or” as used herein refers to and encompasses any and all possible combinations of one or more of the associated listed items. It will be further understood that the terms “comprises” and/or “comprising,” when used in this specification, specify the presence of stated features, integers, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and/or groups thereof. Furthermore, to the extent that the terms “including,” “includes,” “having,” “has,” “with,” or variants thereof are used in either the detailed description and/or the claims, such terms are intended to be inclusive in a manner similar to the term “comprising.”

As used herein, the term “if” may be construed to mean “when” or “upon” or “in response to determining” or “in response to detecting,” depending on the context. Similarly, the phrase “if it is determined” or “if [a stated condition or event] is detected” may be construed to mean “upon determining” or “in response to determining” or “upon detecting [the stated condition or event]” or “in response to detecting [the stated condition or event],” depending on the context.

It will also be understood that, although the terms first, second, etc. may be used herein to describe various elements, these elements should not be limited by these terms. These terms are only used to distinguish one element from another. For example, a first subject could be termed a second subject, and, similarly, a second subject could be termed a first subject, without departing from the scope of the present disclosure. The first subject and the second subject are both subjects, but they are not the same subject. Furthermore, the terms “subject,” “user,” and “patient” are used interchangeably herein.

As used herein, the term “organoid” refers to an in vitro three-dimensional multicellular construct that is developed from stem cells (e.g., embryonic stem cells, induced pluripotent stem cells, and somatic stem cells or tissue derived progenitor cells) or cancer cells in a specific 3D organoid culture system. Organoids contain multiple cells types of the in vivo counter parts and organize similarly to the primary tissue. In some embodiments, the organoid culture system includes an organoid culture medium and an extracellular matrix or extracellular matrix substitute. An “organoid cell line” refers to a plurality of organoids that are derived and established from the same cell or cell population. A “tumor organoid” refers to an organoid derived from a tumor cell or population of tumor cells.

As used herein, the term “subject” refers to any living or non-living human. In some embodiments, a subject is a male or female of any stage (e.g., a man, a women or a child).

As used herein, the terms “control,” “control sample,” “reference,” “reference sample,” “normal,” and “normal sample” describe a sample from a subject that does not have a particular condition, or is otherwise healthy. In an example, a method as disclosed herein can be performed on a subject having a tumor, where the reference sample is a sample taken from a healthy tissue of the subject. A reference sample can be obtained from the subject, or from a database. The reference can be, e.g., a reference genome that is used to map sequence reads obtained from sequencing a sample from the subject. A reference genome can refer to a haploid or diploid genome to which sequence reads from the biological sample and a constitutional sample can be aligned and compared. An example of constitutional sample can be DNA of white blood cells obtained from the subject. For a haploid genome, there can be only one nucleotide at each locus. For a diploid genome, heterozygous loci can be identified; each heterozygous locus can have two alleles, where either allele can allow a match for alignment to the locus.

As used herein, the term “locus” refers to a position (e.g., a site) within a genome, e.g., on a particular chromosome. In some embodiments, a locus refers to a single nucleotide position within a genome, i.e., on a particular chromosome. In some embodiments, a locus refers to a small group of nucleotide positions within a genome, e.g., as defined by a mutation (e.g., substitution, insertion, or deletion) of consecutive nucleotides within a cancer genome. Because normal mammalian cells have diploid genomes, a normal mammalian genome (e.g., a human genome) will generally have two copies of every locus in the genome, or at least two copies of every locus located on the autosomal chromosomes, e.g., one copy on the maternal autosomal chromosome and one copy on the paternal autosomal chromosome.

As used herein, the term “allele” refers to a particular sequence of one or more nucleotides at a chromosomal locus.

As used herein, the term “reference allele” refers to the sequence of one or more nucleotides at a chromosomal locus that is either the predominant allele represented at that chromosomal locus within the population of the species (e.g., the “wild-type” sequence), or an allele that is predefined within a reference genome for the species.

As used herein, the term “variant allele” refers to a sequence of one or more nucleotides at a chromosomal locus that is either not the predominant allele represented at that chromosomal locus within the population of the species (e.g., not the “wild-type” sequence), or not an allele that is predefined within a reference genome for the species.

As used herein, the term “single nucleotide variant” or “SNV” refers to a substitution of one nucleotide to a different nucleotide at a position (e.g., site) of a nucleotide sequence, e.g., a sequence read from an individual. A substitution from a first nucleobase X to a second nucleobase Y may be denoted as “X>Y.” For example, a cytosine to thymine SNV may be denoted as “C>T.”

As used herein, the term “mutation” or “variant” refers to a detectable change in the genetic material of one or more cells. In a particular example, one or more mutations can be found in, and can identify, cancer cells (e.g., driver and passenger mutations). A mutation can be transmitted from apparent cell to a daughter cell. A person having skill in the art will appreciate that a genetic mutation (e.g., a driver mutation) in a parent cell can induce additional, different mutations (e.g., passenger mutations) in a daughter cell. A mutation generally occurs in a nucleic acid. In a particular example, a mutation can be a detectable change in one or more deoxyribonucleic acids or fragments thereof. A mutation generally refers to nucleotides that is added, deleted, substituted for, inverted, or transposed to a new position in a nucleic acid. A mutation can be a spontaneous mutation or an experimentally induced mutation. A mutation in the sequence of a particular tissue is an example of a “tissue-specific allele.” For example, a tumor can have a mutation that results in an allele at a locus that does not occur in normal cells. Another example of a “tissue-specific allele” is a fetal-specific allele that occurs in the fetal tissue, but not the maternal tissue.

As used herein the term “cancer,” “cancerous tissue,” or “tumor” refers to an abnormal mass of tissue in which the growth of the mass surpasses and is not coordinated with the growth of normal tissue. A cancer or tumor can be defined as “benign” or “malignant” depending on the following characteristics: degree of cellular differentiation including morphology and functionality, rate of growth, local invasion and metastasis. A “benign” tumor can be well differentiated, have characteristically slower growth than a malignant tumor and remain localized to the site of origin. In addition, in some cases a benign tumor does not have the capacity to infiltrate, invade or metastasize to distant sites. A “malignant” tumor can be a poorly differentiated (anaplasia), have characteristically rapid growth accompanied by progressive infiltration, invasion, and destruction of the surrounding tissue. Furthermore, a malignant tumor can have the capacity to metastasize to distant sites. Accordingly, a cancer cell is a cell found within the abnormal mass of tissue whose growth is not coordinated with the growth of normal tissue. Accordingly, a “tumor sample” refers to a biological sample obtained or derived from a tumor of a subject, as described herein.

As used herein, the terms “sequencing,” “sequence determination,” and the like as used herein refers generally to any and all biochemical processes that may be used to determine the order of biological macromolecules such as nucleic acids or proteins. For example, sequencing data can include all or a portion of the nucleotide bases in a nucleic acid molecule such as an mRNA transcript or a genomic locus.

As used herein, the term “sequence reads” or “reads” refers to nucleotide sequences produced by any sequencing process described herein or known in the art. Reads can be generated from one end of nucleic acid fragments (“single-end reads”), and sometimes are generated from both ends of nucleic acids (e.g., paired-end reads, double-end reads). The length of the sequence read is often associated with the particular sequencing technology. High-throughput methods, for example, provide sequence reads that can vary in size from tens to hundreds of base pairs (bp). In some embodiments, the sequence reads are of a mean, median or average length of about 15 bp to 900 bp long (e.g., about 20 bp, about 25 bp, about 30 bp, about 35 bp, about 40 bp, about 45 bp, about 50 bp, about 55 bp, about 60 bp, about 65 bp, about 70 bp, about 75 bp, about 80 bp, about 85 bp, about 90 bp, about 95 bp, about 100 bp, about 110 bp, about 120 bp, about 130, about 140 bp, about 150 bp, about 200 bp, about 250 bp, about 300 bp, about 350 bp, about 400 bp, about 450 bp, or about 500 bp. In some embodiments, the sequence reads are of a mean, median or average length of about 1000 bp, 2000 bp, 5000 bp, 10,000 bp, or 50,000 bp or more. Nanopore sequencing, for example, can provide sequence reads that can vary in size from tens to hundreds to thousands of base pairs. Illumina parallel sequencing can provide sequence reads that do not vary as much, for example, most of the sequence reads can be smaller than 200 bp. A sequence read (or sequencing read) can refer to sequence information corresponding to a nucleic acid molecule (e.g., a string of nucleotides). For example, a sequence read can correspond to a string of nucleotides (e.g., about 20 to about 150) from part of a nucleic acid fragment, can correspond to a string of nucleotides at one or both ends of a nucleic acid fragment, or can correspond to nucleotides of the entire nucleic acid fragment. A sequence read can be obtained in a variety of ways, e.g., using sequencing techniques or using probes, e.g., in hybridization arrays or capture probes, or amplification techniques, such as the polymerase chain reaction (PCR) or linear amplification using a single primer or isothermal amplification.

As used herein, the term “read segment” or “read” refers to any nucleotide sequences including sequence reads obtained from an individual and/or nucleotide sequences derived from the initial sequence read from a sample obtained from an individual. For example, a read segment can refer to an aligned sequence read, a collapsed sequence read, or a stitched read. Furthermore, a read segment can refer to an individual nucleotide base, such as a single nucleotide variant.

As used herein, the term, “reference exome” refers to any particular known, sequenced or characterized exome, whether partial or complete, of any tissue from any organism or pathogen that may be used to reference identified sequences from a subject. Example reference exomes used for human subjects as well as many other organisms are provided in the on-line genome browser hosted by the National Center for Biotechnology Information (“NCBI”).

As used herein, the term “reference genome” refers to any particular known, sequenced or characterized genome, whether partial or complete, of any organism or pathogen that may be used to reference identified sequences from a subject. Exemplary reference genomes used for human subjects as well as many other organisms are provided in the on-line genome browser hosted by the National Center for Biotechnology Information (“NCBI”) or the University of California, Santa Cruz (UCSC). A “genome” refers to the complete genetic information of an organism or pathogen, expressed in nucleic acid sequences. As used herein, a reference sequence or reference genome often is an assembled or partially assembled genomic sequence from an individual or multiple individuals. In some embodiments, a reference genome is an assembled or partially assembled genomic sequence from one or more human individuals. The reference genome can be viewed as a representative example of a species' set of genes. In some embodiments, a reference genome comprises sequences assigned to chromosomes. Exemplary human reference genomes include but are not limited to NCBI build 34 (UCSC equivalent: hg16), NCBI build 35 (UCSC equivalent: hg17), NCBI build 36.1 (UCSC equivalent: hg18), GRCh37 (UCSC equivalent: hg19), and GRCh38 (UCSC equivalent: hg38).

As used herein, the term “assay” refers to a technique for determining a property of a substance, e.g., a nucleic acid, a protein, a cell, a tissue, or an organ. An assay (e.g., a first assay or a second assay) can comprise a technique for determining the copy number variation of nucleic acids in a sample, the methylation status of nucleic acids in a sample, the fragment size distribution of nucleic acids in a sample, the mutational status of nucleic acids in a sample, or the fragmentation pattern of nucleic acids in a sample. Any assay known to a person having ordinary skill in the art can be used to detect any of the properties of nucleic acids mentioned herein. Properties of a nucleic acids can include a sequence, genomic identity, copy number, methylation state at one or more nucleotide positions, size of the nucleic acid, presence or absence of a mutation in the nucleic acid at one or more nucleotide positions, and pattern of fragmentation of a nucleic acid (e.g., the nucleotide position(s) at which a nucleic acid fragments). An assay or method can have a particular sensitivity and/or specificity, and their relative usefulness as a diagnostic tool can be measured using ROC-AUC statistics.

The term “classification” can refer to any number(s) or other characters(s) that are associated with a particular property of a sample. For example, in some embodiments, the term “classification” can refer to a type of cancer in a subject or sample, a stage of cancer in a subject or sample, a prognosis for a cancer in a subject or sample, a tumor load in a subject, a presence of tumor metastasis in a subject, and the like. The classification can be binary (e.g., positive or negative) or have more levels of classification (e.g., a scale from 1 to 10 or 0 to 1). The terms “cutoff” and “threshold” can refer to predetermined numbers used in an operation. For example, a cutoff size can refer to a size above which fragments are excluded. A threshold value can be a value above or below which a particular classification applies. Either of these terms can be used in either of these contexts.

Several aspects are described below with reference to example applications for illustration. It should be understood that numerous specific details, relationships, and methods are set forth to provide a full understanding of the features described herein. One having ordinary skill in the relevant art, however, will readily recognize that the features described herein can be practiced without one or more of the specific details or with other methods. The features described herein are not limited by the illustrated ordering of acts or events, as some acts can occur in different orders and/or concurrently with other acts or events. Furthermore, not all illustrated acts or events are required to implement a methodology in accordance with the features described herein.

Reference will now be made in detail to embodiments, examples of which are illustrated in the accompanying drawings. In the following detailed description, numerous specific details are set forth in order to provide a thorough understanding of the present disclosure. However, it will be apparent to one of ordinary skill in the art that the present disclosure may be practiced without these specific details. In other instances, well-known methods, procedures, components, circuits, and networks have not been described in detail so as not to unnecessarily obscure aspects of the embodiments.

Example System Embodiments.

Now that an overview of some aspects of the present disclosure and some definitions used in the present disclosure have been provided, details of an exemplary system are now described in conjunction with FIG. 1 . FIG. 1 is a block diagram illustrating a system 100 in accordance with some implementations. The device 100 in some implementations includes one or more processing units CPU(s) 102 (also referred to as processors), one or more network interfaces 104, a user interface 106, a non-persistent memory 111, a persistent memory 112, and one or more communication buses 114 for interconnecting these components. The one or more communication buses 114 optionally include circuitry (sometimes called a chipset) that interconnects and controls communications between system components. The non-persistent memory 111 typically includes high-speed random access memory, such as DRAM, SRAM, DDR RAM, ROM, EEPROM, flash memory, whereas the persistent memory 112 typically includes CD-ROM, digital versatile disks (DVD) or other optical storage, magnetic cassettes, magnetic tape, magnetic disk storage or other magnetic storage devices, magnetic disk storage devices, optical disk storage devices, flash memory devices, or other non-volatile solid state storage devices. The persistent memory 112 optionally includes one or more storage devices remotely located from the CPU(s) 102. The persistent memory 112, and the non-volatile memory device(s) within the non-persistent memory 112, comprise non-transitory computer readable storage medium. In some implementations, the non-persistent memory 111 or alternatively the non-transitory computer readable storage medium stores the following programs, modules and data structures, or a subset thereof, sometimes in conjunction with the persistent memory 112:

-   -   an optional operating system 116, which includes procedures for         handling various basic system services and for performing         hardware dependent tasks;     -   an optional network communication module (or instructions) 118         for connecting the system 100 with other devices and/or a         communication network;     -   a test subject data store 120 for storing datasets containing         biological information and/or personal characteristics about         test subjects, including sequencing data 122, nucleic acid         features 124, personal characteristics 126, and/or organoid         sensitivities 128;     -   an optional classifier training module 130 for training         classifiers, e.g., to distinguish between disease states or         predicted treatment outcomes, for example, based on information         learned from studies of patient-based organoid cultures;     -   an optional disease classification module 130 for classifying         the cancer status of a subject based on test subject data, e.g.,         sequencing data 122, nucleic acid features 124, personal         characteristics 126, and/or patient-derived organoid         sensitivities 128 stored in test subject data store 120;     -   an optional drug classification module 150 for classifying a         utility of a therapeutic compound based on organoid-derived         sensitivities to the therapeutic compound; and     -   an optional patient reporting module 160 for generating reports         about the disease (e.g., cancer) status of a test subject.

In various implementations, one or more of the above identified elements are stored in one or more of the previously mentioned memory devices, and correspond to a set of instructions for performing a function described above. The above identified modules, data, or programs (e.g., sets of instructions) need not be implemented as separate software programs, procedures, datasets, or modules, and thus various subsets of these modules and data may be combined or otherwise re-arranged in various implementations.

In some implementations, the non-persistent memory 111 optionally stores a subset of the modules and data structures identified above. Furthermore, in some embodiments, the memory stores additional modules and data structures not described above. In some embodiments, one or more of the above identified elements is stored in a computer system, other than that of system 100, that is addressable by system 100 so that system 100 may retrieve all or a portion of such data when needed.

Although FIG. 1 depicts a “system 100,” the figure is intended more as functional description of the various features which may be present in one or more computer systems than as a structural schematic of the implementations described herein. In practice, and as recognized by those of ordinary skill in the art, items shown separately could be combined and some items could be separated. Moreover, although FIG. 1 depicts certain data and modules in non-persistent memory 111, some or all of these data and modules may be in persistent memory 112.

For instance, as depicted in FIG. 2 , in some embodiments the methods described herein are performed across a distributed diagnostic environment 210, e.g., connected via communication network 212. In some embodiments, one or more biological sample, e.g., one or more tumor biopsy or control sample, is collected from a subject in clinical environment 220, e.g., a doctor's office, hospital, or medical clinic. In some embodiments, a portion of the sample is processed within the clinical environment using a processing device 224, e.g., a nucleic acid sequencer for obtaining sequencing data, a microscope for obtaining pathology data, a mass spectrometer for obtaining proteomic data, etc. In some embodiments, the biological sample or a portion of the biological sample is sent to one or more external environments, e.g., sequencing lab 230, pathology lab 240, and molecular biology lab 250, each of which includes a processing device 234, 244, and 254, respectively, to generate biological data about the subject. Each environment includes a communications device 222, 232, 242, and 252, respectively, for communicating biological data about the subject to a processing server 262 and/or database 264, which may located in yet another environment, e.g., processing/storage center 260. Thus, in some embodiments, different portions of the systems and methods described herein are fulfilled by different processing devices located in different physical environments.

Classifiers

In some embodiments, the methods described herein use biological features, e.g., genomic features, of a subject and/or cultured organoid, e.g., a patient-specific tumor organoid, to classify a condition, e.g., cancer, predicted an effect of a particular therapy, etc. Generally, any classifier architecture can be trained for these purposes. Non-limiting examples of classifier types that can be used in conjunction with the methods described herein include a machine learning algorithm, a neural network algorithm, a support vector machine algorithm, a decision tree algorithm, an unsupervised clustering model algorithm, a supervised clustering model algorithm, or a regression model. In some embodiments, the trained classifier is binomial or multinomial.

In some embodiments, the classifier is implemented as an artificial intelligence engine and may include gradient boosting models, random forest models, neural networks (NN), regression models, Naive Bayes models, and/or machine learning algorithms (MLA). MLAs include supervised algorithms (such as algorithms where the features/classifications in the data set are annotated) using linear regression, logistic regression, decision trees, classification and regression trees, naive Bayes, nearest neighbor clustering; unsupervised algorithms (such as algorithms where no features/classification in the data set are annotated) using apriori, means clustering, principal component analysis, random forest, adaptive boosting; and semi-supervised algorithms (such as algorithms where an incomplete number of features/classifications in the data set are annotated) using generative approach (such as a mixture of Gaussian distributions, mixture of multinomial distributions, hidden Markov models), low density separation, graph-based approaches (such as mincut, harmonic function, manifold regularization), heuristic approaches, or support vector machines.

While MLA and neural networks identify distinct approaches to machine learning, the terms may be used interchangeably herein. Thus, a mention of MLA may include a corresponding NN or a mention of NN may include a corresponding MLA unless explicitly stated otherwise. Training may include providing optimized datasets, labeling these traits as they occur in patient records, and training the MLA to predict or classify based on new inputs. Artificial NNs are efficient computing models which have shown their strengths in solving hard problems in artificial intelligence. They have also been shown to be universal approximators, that is, they can represent a wide variety of functions when given appropriate parameters.

Neural network (NN) algorithms, including convolutional neural network algorithms, that can serve as the classifier for the instant methods are disclosed in See, Vincent et al., 2010, “Stacked denoising autoencoders: Learning useful representations in a deep network with a local denoising criterion,” J Mach Learn Res 11, pp. 3371-3408; Larochelle et al., 2009, “Exploring strategies for training deep neural networks,” J Mach Learn Res 10, pp. 1-40; and Hassoun, 1995, Fundamentals of Artificial Neural Networks, Massachusetts Institute of Technology, each of which is hereby incorporated by reference. NNs include conditional random fields, convolutional neural networks, attention based neural networks, deep learning, long short term memory networks, or other neural models.

Example logistic regression algorithms are disclosed in Agresti, An Introduction to Categorical Data Analysis, 1996, Chapter 5, pp. 103-144, John Wiley & Son, New York, which is hereby incorporated by reference.

Support vector machine (SVM) algorithms that can serve as the classifier for the instant methods are described in Cristianini and Shawe-Taylor, 2000, “An Introduction to Support Vector Machines,” Cambridge University Press, Cambridge; Boser et al., 1992, “A training algorithm for optimal margin classifiers,” in Proceedings of the 5^(th) Annual ACM Workshop on Computational Learning Theory, ACM Press, Pittsburgh, Pa., pp. 142-152; Vapnik, 1998, Statistical Learning Theory, Wiley, New York; Mount, 2001, Bioinformatics: sequence and genome analysis, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Duda, Pattern Classification, Second Edition, 2001, John Wiley & Sons, Inc., pp. 259, 262-265; and Hastie, 2001, The Elements of Statistical Learning, Springer, New York; and Furey et al., 2000, Bioinformatics 16, 906-914, each of which is hereby incorporated by reference in its entirety. When used for classification, SVMs separate a given set of binary-labeled data training set with a hyper-plane that is maximally distant from the labeled data. For cases in which no linear separation is possible, SVMs can work in combination with the technique of ‘kernels’, which automatically realizes a non-linear mapping to a feature space. The hyper-plane found by the SVM in feature space corresponds to a non-linear decision boundary in the input space.

Decision trees (e.g., random forest, boosted trees) that can serve as the classifier for the instant methods are described generally by Duda, 2001, Pattern Classification, John Wiley & Sons, Inc., New York, pp. 395-396, which is hereby incorporated by reference. Tree-based methods partition the feature space into a set of rectangles, and then fit a model (like a constant) in each one. In some embodiments, the decision tree is random forest regression. One specific algorithm that can serve as the classifier for the instant methods is a classification and regression tree (CART). Other specific decision tree algorithms that can serve as the classifier for the instant methods include, but are not limited to, ID3, C4.5, MART, and Random Forests. CART, ID3, and C4.5 are described in Duda, 2001, Pattern Classification, John Wiley & Sons, Inc., New York, pp. 396-408 and pp. 411-412, which is hereby incorporated by reference. CART, MART, and C4.5 are described in Hastie et al., 2001, The Elements of Statistical Learning, Springer-Verlag, New York, Chapter 9, which is hereby incorporated by reference in its entirety. Random Forests are described in Breiman, 1999, “Random Forests—Random Features,” Technical Report 567, Statistics Department, U.C. Berkeley, September 1999, which is hereby incorporated by reference in its entirety.

Biological Samples

In some embodiments, one or more biological samples collected from a subject is a solid tissue sample, e.g., a solid tumor sample or a solid normal tissue sample. Methods for obtaining solid tissue samples, e.g., of cancerous and/or normal tissue are known in the art, and are dependent upon the type of tissue being sampled. For example, bone marrow biopsies and isolation of circulating tumor cells can be used to obtain samples of blood cancers, endoscopic biopsies can be used to obtain samples of cancers of the digestive tract, bladder, and lungs, needle biopsies (e.g., fine-needle aspiration, core needle aspiration, vacuum-assisted biopsy, and image-guided biopsy, can be used to obtain samples of subdermal tumors, skin biopsies, e.g., shave biopsy, punch biopsy, incisional biopsy, and excisional biopsy, can be used to obtain samples of dermal cancers, and surgical biopsies can be used to obtain samples of cancers affecting internal organs of a patient. In some embodiments, a solid tissue sample is a formalin-fixed tissue (FFT). In some embodiments, a solid tissue sample is a macro-dissected formalin fixed paraffin embedded (FFPE) tissue. In some embodiments, a solid tissue sample is a fresh frozen tissue sample.

In some embodiments, one or more of the biological samples collected from a subject is a liquid biological sample, also referred to as a liquid biopsy sample. In some embodiments, one or more of the biological samples obtained from the patient are selected from blood, plasma, serum, urine, vaginal fluid, fluid from a hydrocele (e.g., of the testis), vaginal flushing fluids, pleural fluid, ascitic fluid, cerebrospinal fluid, saliva, sweat, tears, sputum, bronchoalveolar lavage fluid, discharge fluid from the nipple, aspiration fluid from different parts of the body (e.g., thyroid, breast), etc. In some embodiments, the liquid biopsy sample includes blood and/or saliva. In some embodiments, the liquid biopsy sample is peripheral blood. In some embodiments, blood samples are collected from patients in commercial blood collection containers, e.g., using a PAXgene® Blood DNA Tubes. In some embodiments, saliva samples are collected from patients in commercial saliva collection containers, e.g., using an Oragene® DNA Saliva Kit.

Liquid biopsy samples include cell free nucleic acids, including cell-free DNA (cfDNA). As described above, cfDNA isolated from cancer patients includes DNA originating from cancerous cells, also referred to as circulating tumor DNA (ctDNA), cfDNA originating from germline (e.g., healthy or non-cancerous) cells, and cfDNA originating from hematopoietic cells (e.g., white blood cells). The relative proportions of cancerous and non-cancerous cfDNA present in a liquid biopsy sample varies depending on the characteristics (e.g., the type, stage, lineage, genomic profile, etc.) of the patient's cancer.

cfDNA is a particularly useful source of biological data for various implementations of the methods and systems described herein, because it is readily obtained from various body fluids. Advantageously, use of bodily fluids facilitates serial monitoring because of the ease of collection, as these fluids are collectable by non-invasive or minimally-invasive methodologies. This is in contrast to methods that rely upon solid tissue samples, such as biopsies, which often times require invasive surgical procedures. Further, because bodily fluids, such as blood, circulate throughout the body, the cfDNA population represents a sampling of many different tissue types from many different locations.

In some embodiments, a liquid biopsy sample is separated into two different samples. For example in some embodiments, a blood sample is separated into a blood plasma sample, containing cfDNA, and a buffy coat preparation, containing white blood cells.

In some embodiments, a dedicated normal sample is also collected from a subject, for co-processing with a solid or liquid cancer sample. Generally, the normal sample is of a non-cancerous tissue, and can be collected using any tissue collection means described above. In some embodiments, buccal cells collected from the inside of a patient's cheeks are used as a normal sample. Buccal cells can be collected by placing an absorbent material, e.g., a swab, in the subjects mouth and rubbing it against their cheek, e.g., for at least 15 second or for at least 30 seconds. The swab is then removed from the patient's mouth and inserted into a tube, such that the tip of the tube is submerged into a liquid that serves to extract the buccal cells off of the absorbent material. An example of buccal cell recovery and collection devices is provided in U.S. Pat. No. 9,138,205, the content of which is hereby incorporated by reference, in its entirety, for all purposes. In some embodiments, the buccal swab DNA is used as a source of normal DNA in circulating heme malignancies.

The biological samples collected from the patient are, optionally, sent to various analytical environments (e.g., sequencing lab 230, pathology lab 240, and/or molecular biology lab 250) for processing (e.g., data collection) and/or analysis (e.g., feature extraction). Wet lab processing 204 may include cataloguing samples (e.g., accessioning), examining clinical features of one or more samples (e.g., pathology review), and nucleic acid sequence analysis (e.g., extraction, library prep, capture +hybridize, pooling, and sequencing). In some embodiments, the workflow includes clinical analysis of one or more biological samples collected from the subject, e.g., at a pathology lab 240 and/or a molecular and cellular biology lab 250, to generate clinical features such as pathology features 128-3, imaging data 128-3, and/or tissue culture/organoid data 128-3.

Feature Extraction

In some embodiments, tissue culture/organoid data includes features identified by evaluation of cultured tissue from the subject. For instance, in some embodiments, tissue samples obtained from the patients (e.g., tumor tissue, normal tissue, or both) are cultured (e.g., in liquid culture, solid-phase culture, and/or organoid culture) and various features, such as cell morphology, growth characteristics, genomic alterations, and/or drug sensitivity, are evaluated. In some embodiments, tissue culture/organoid data 128-3 includes features determined using machine learning algorithms to evaluate tissue culture/organoid data collected as described herein. Genetic sequencing used to generate the features used in the methods described herein may be done on either a tumor organoid, e.g., cultured from cells of a test subject, or the source tissue (patient biopsy used to generate the TO), e.g., to determine the tumor organoid's (e.g., the subject's cancer) BRCA1/2 mutation status, loss of heterozygocity, bi-allelic loss status, etc.

In some embodiments of the methods described herein, nucleic acid sequencing of one or more samples, e.g., a biological sample from a subject and/or a tissue culture/organoid sample, is performed. Briefly, nucleic acids, e.g., RNA and/or DNA are extracted (304) from the one or more biological samples. Methods for isolating nucleic acids from biological samples are known in the art, and are dependent upon the type of nucleic acid being isolated (e.g., cfDNA, DNA, and/or RNA) and the type of sample from which the nucleic acids are being isolated (e.g., liquid biopsy samples, white blood cell buffy coat preparations, formalin-fixed paraffin-embedded (FFPE) solid tissue samples, and fresh frozen solid tissue samples). The selection of any particular nucleic acid isolation technique for use in conjunction with the embodiments described herein is well within the skill of the person having ordinary skill in the art, who will consider the sample type, the state of the sample, the type of nucleic acid being sequenced and the sequencing technology being used.

For instance, many techniques for DNA isolation, e.g., genomic DNA isolation, from a tissue sample are known in the art, such as organic extraction, silica adsorption, and anion exchange chromatography. Likewise, many techniques for RNA isolation, e.g., mRNA isolation, from a tissue sample are known in the art. For example, acid guanidinium thiocyanate-phenol-chloroform extraction (see, for example, Chomczynski and Sacchi, 2006, Nat Protoc, 1(2):581-85, which is hereby incorporated by reference herein), and silica bead/glass fiber adsorption (see, for example, Poeckh, T. et al., 2008, Anal Biochem., 373(2):253-62, which is hereby incorporated by reference herein). The selection of any particular DNA or RNA isolation technique for use in conjunction with the embodiments described herein is well within the skill of the person having ordinary skill in the art, who will consider the tissue type, the state of the tissue, e.g., fresh, frozen, formalin-fixed, paraffin-embedded (FFPE), and the type of nucleic acid analysis that is to be performed.

In some embodiments, a nucleic acid library is prepared from the isolated nucleic acids (e.g., cfDNA, DNA, and/or RNA). For example, in some embodiments, DNA libraries (e.g., gDNA and/or cfDNA libraries) are prepared from isolated DNA from the one or more biological samples. In some embodiments, the DNA libraries are prepared using a commercial library preparation kit, e.g., the KAPA Hyper Prep Kit, a New England Biolabs (NEB) kit, or a similar kit.

In some embodiments, during library preparation, adapters (e.g., UDI adapters, such as Roche SeqCap dual end adapters, or UMI adapters such as full length or stubby Y adapters) are ligated onto the nucleic acid molecules. In some embodiments, the adapters include unique molecular identifiers (UMIs), which are short nucleic acid sequences (e.g., 3-10 base pairs) that are added to ends of DNA fragments during adapter ligation. In some embodiments, UMIs are degenerate base pairs that serve as a unique tag that can be used to identify sequence reads originating from a specific DNA fragment. In some embodiments, e.g., when multiplex sequencing will be used to sequence DNA from a plurality of samples (e.g., from the same or different subjects) in a single sequencing reaction, a patient-specific index is also added to the nucleic acid molecules. In some embodiments, the patient specific index is a short nucleic acid sequence (e.g., 3-20 nucleotides) that are added to ends of DNA fragments during library construction, that serve as a unique tag that can be used to identify sequence reads originating from a specific patient sample. Examples of identifier sequences are described, for example, in Kivioja et al., Nat. Methods 9(1):72-74 (2011) and Islam et al., Nat. Methods 11(2):163-66 (2014), the contents of which are hereby incorporated by reference, in their entireties, for all purposes.

In some embodiments, an adapter includes a PCR primer landing site, designed for efficient binding of a PCR or second-strand synthesis primer used during the sequencing reaction. In some embodiments, an adapter includes an anchor binding site, to facilitate binding of the DNA molecule to anchor oligonucleotide molecules on a sequencer flow cell, serving as a seed for the sequencing process by providing a starting point for the sequencing reaction. During PCR amplification following adapter ligation, the UMIs, patient indexes, and binding sites are replicated along with the attached DNA fragment. This provides a way to identify sequence reads that came from the same original fragment in downstream analysis.

In some embodiments, a sequencing library, or pool of sequencing libraries, is enriched for target nucleic acids, e.g., nucleic acids encompassing loci that are informative for precision oncology and/or used as internal controls for sequencing or bioinformatics processes. In some embodiments, enrichment is achieved by hybridizing target nucleic acids in the sequencing library to probes that hybridize to the target sequences, and then isolating the captured nucleic acids away from off-target nucleic acids that are not bound by the capture probes.

In some embodiments, e.g., where a whole genome sequencing method will be used, nucleic acid sequencing libraries are not target-enriched prior to sequencing, in order to obtain sequencing data on substantially all of the competent nucleic acids in the sequencing library. Similarly, in some embodiments, e.g., where a whole genome sequencing method will be used, nucleic acid sequencing libraries are not mixed, because of bandwidth limitations related to obtaining significant sequencing depth across an entire genome. However, in other embodiments, e.g., where a low pass whole genome sequencing (LPWGS) methodology will be used, nucleic acid sequencing libraries can still be pooled, because very low average sequencing coverage is achieved across a respective genome, e.g., between about 0.5× and about 5×.

In some embodiments, the probe set includes probes targeting one or more gene loci, e.g., exon or intron loci. In some embodiments, the probe set includes probes targeting one or more loci not encoding a protein, e.g., regulatory loci, miRNA loci, and other non-coding loci, e.g., that have been found to be associated with cancer. In some embodiments, the plurality of loci include at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 500, 750, 1000, 2500, 5000, or more human genomic loci. In some embodiments, the gene panel is a whole-exome panel that analyzes the exomes of a biological sample. In some embodiments, the gene panel is a whole-genome panel that analyzes the genome of a specimen.

Sequence reads are then generated from the sequencing library or pool of sequencing libraries. Sequencing data may be acquired by any methodology known in the art. For example, next generation sequencing (NGS) techniques such as sequencing-by-synthesis technology (Illumina), pyrosequencing (454 Life Sciences), ion semiconductor technology (Ion Torrent sequencing), single-molecule real-time sequencing (Pacific Biosciences), sequencing by ligation (SOLiD sequencing), nanopore sequencing (Oxford Nanopore Technologies), or paired-end sequencing. In some embodiments, massively parallel sequencing is performed using sequencing-by-synthesis with reversible dye terminators. In some embodiments, sequencing is performed using next generation sequencing technologies, such as short-read technologies. In other embodiments, long-read sequencing or another sequencing method known in the art is used.

In some embodiments, the methods described herein include one or more of obtaining a biological sample, extracting nucleic acids from the biological sample, and sequencing the isolated nucleic acids. In other embodiments, sequencing data or feature data sets obtained therefrom used in the improved systems and methods described herein are obtained by receiving previously generated sequence reads or feature data sets, in electronic form.

In some embodiments, the methods and systems described herein use additional features to perform the various classifications provided herein. Non-limiting examples of other characteristics that may be used for these purposes include tumor organoid histology, and baseline histology (H&E image; features; see also Patent Application Nos. 62/787,047 and 62/824,039); clinical data (gender, age, family medical history, personal history of cancer, treatment history of cancer, diagnosis, subtype, IHC markers, DNA/RNA sequence); methylation sequence; radiology images/features; comorbidities, geographic location, ancestry, ethnic features, diet, gut microbiome, substance usage, alcohol use, physical exam findings, baseline vitals, vaccination history, religious or cultural beliefs, marital status, sexual orientation, nocturnal/diurnal rhythm, sleep schedule, travel history (including airplane travel), travel to certain regions, presence/absence of parasitic organisms, infectious disease history (including parasitic organisms, viruses, bacteria), germline DNA sequence, biometric features (like distance between eyes, bones), skull shape, physical profile, occupational history, living with pets (including birds), mental health; tumor organoid morphology; viability; and smoking status.

Evaluation of BRCA1-/BRCA2-cancers for PARPi Treatment Using Tumor Organoid Cultures

In one aspect, the disclosure provides methods and systems for performing methods of evaluating a cancer that does not carry either a BRCA1 or a BRCA2 mutation in a test subject by determining a sensitivity of the cancer to a poly ADP ribose polymerase (PARP) inhibitor. The method includes culturing a plurality of tumor organoids, each respective tumor organoid in the plurality of tumor organoids from one or more cells of a tumor biopsy from the test subject. The method then includes exposing the one or more cultured organoids to one or more amounts of the PARP inhibitor. The method then includes measuring the fitness of cells in the one or more tumor organoids following the exposure to the one or more amounts of the PARP inhibitor. The method then includes correlating the measured fitness of the cells with a sensitivity to the PARP inhibitor.

In some embodiments, the method also includes providing a recommendation for treatment of the subject. For example, in some embodiments, when the correlated sensitivity to the PARP inhibitor satisfies a sensitivity threshold, the method includes communicating a recommended therapy comprising the PARP inhibitor to the test subject, and when the correlated sensitivity to the PARP inhibitor does not satisfy a sensitivity threshold, the method includes communicating a recommended therapy that does not include the PARP inhibitor to the test subj ect.

In some embodiments, the method also includes prescribing therapy for treating the cancer in the subject. For example, in some embodiments, when the correlated sensitivity to the PARP inhibitor satisfies a sensitivity threshold, the method includes prescribing a therapy including the PARP inhibitor to the test subject, and when the correlated sensitivity to the PARP inhibitor does not satisfy a sensitivity threshold, the method includes prescribing a therapy that does not include the PARP inhibitor to the test subject.

In some embodiments, the method also includes treating the cancer in the subject. For example, in some embodiments, when the correlated sensitivity to the PARP inhibitor satisfies a sensitivity threshold, the method includes administering a therapy including the PARP inhibitor to the test subject, and when the correlated sensitivity to the PARP inhibitor does not satisfy a sensitivity threshold, the method includes administering a therapy that does not include the PARP inhibitor to the test subject.

In some embodiments, the cancer is a breast cancer. In some embodiments, the cancer is an ovarian cancer. In some embodiments, the cancer is not breast cancer or ovarian cancer. In some embodiments, the test subject has not previously been treated for cancer. That is, in some embodiments, the PARP inhibitor is administered as a first-line therapy. In some embodiments, the test subject has been previously treated for the cancer. That is, in some embodiments, the PARP inhibitor is administered as a second-line therapy. In some embodiments, the PARP inhibitor is olaparib, veliparib, rucaparib, niraparib, or talazoparib.

Training a Classifier to Evaluate PARPi Sensitivity

In one aspect, the disclosure provides methods and systems for performing methods of training a classifier to discriminate between two or more tumor sensitivities to a poly ADP ribose polymerase (PARP) inhibitor. In some embodiments, the method includes obtaining a data set comprising, for each respective tissue sample in a plurality of tissue samples, (i) a corresponding plurality of nucleic acid features of the tissue sample, and (ii) a corresponding indication of the sensitivity of a respective organoid cultured from one or more cells of the tissue sample to the PARP inhibitor. The method then includes training an untrained classifier against at least (i) the corresponding plurality of features and (ii) the corresponding indication of the sensitivity of the organoid to the PARP inhibitor, across the plurality of tissue samples, thereby obtaining a trained classifier that discriminates between the two or more tumor sensitivities to a poly ADP ribose polymerase (PARP) inhibitor.

In some embodiments, the two or more tumor sensitivities include a first level of sensitivity to a first PARP inhibitor and a second level of sensitivity to the first PARP inhibitor. In some embodiments, the two or more tumor sensitivities include a first sensitivity to a first PARP inhibitor and a second sensitivity to a second PARP inhibitor.

In some embodiments, the PARP inhibitor is olaparib, veliparib, rucaparib, niraparib, or talazoparib.

In some embodiments, the classifier is further trained to discriminate between the two or more tumor sensitivities to a PARP inhibitor and one or more tumor sensitivity to a chemotherapeutic drug that is not a PARP inhibitor.

In some embodiments, each tissue sample in the plurality of tissue samples was obtained from a subject that had not received treatment for cancer prior to the tissue sample being obtained. In some embodiments, each tissue sample in the plurality of tissue samples is a breast cancer biopsy. In some embodiments, each tissue sample in the plurality of tissue samples is an ovarian cancer biopsy. In some embodiments, each tissue sample in the plurality of tissue samples is a biopsy of a homologous recombination deficient (HRD) cancer. In some embodiments, each tissue sample in the plurality of tissue samples is a biopsy from a cancer other than breast cancer or ovarian cancer.

In some embodiments, the plurality of nucleic acid features of the tissue sample includes one or more of support for a single nucleotide variant at a genomic location, a methylation status at a genomic location, a relative copy number for a genomic location, an allelic ratio for a genomic location, a relative expression level of a gene, and mathematical combinations thereof. In some embodiments, the plurality of nucleic acid features of the tissue sample comprises a BRCA1 or BRCA2 mutant allele status. In some embodiments, at least a sub-plurality of the plurality of nucleic acid features of the tissue sample are measured from a tumor organoid cultured from one or more cells of the tissue sample.

In some embodiments, the indication of the sensitivity of the respective organoid to the PARP inhibitor is based at least in part on one or more cellular fitness measurements obtained by: i) culturing one or more organoids, each respective organoid in the one or more organoids from one or more cells of the respective tissue sample, ii) exposing the one or more organoids cultured in i) to one or more amounts of the PARP inhibitor, and iii) measuring the fitness of cells, e.g., using a cellular viability assay or cell death assay, in the one or more organoids following the exposure to the one or more amounts of the PARP inhibitor, thereby obtaining the one or more cellular fitness measurements.

In some embodiments, the one or more cellular fitness measurements are one or more measurements of cellular apoptosis following exposure to the PARP inhibitor.

In some embodiments, for at least one respective tissue sample in the plurality of tissue samples, the one or more cultured organoids are exposed to a sensitizing therapy, e.g., radiation or a different chemotherapeutic drug, before being exposed to the PARP inhibitor.

In some embodiments, the untrained classifier is further trained against, for each respective tissue sample in the plurality of tissue samples, a corresponding cancer classification of the tissue sample in a plurality of cancer classifications. In some embodiments, the plurality of cancer classifications includes cancerous tissue and non-cancerous tissue. In some embodiments, the plurality of cancer classifications includes a plurality of types of cancer. In some embodiments, the plurality of cancer classifications includes a plurality of stages of cancer.

In some embodiments, the plurality of tissue samples includes a plurality of tumor biopsies, and the classifier training includes identifying a plurality of genes that are differentially expressed between (i) organoids, cultured from one or more cells of a respective tumor biopsy in the plurality of tumor biopsies, that have a first sensitivity to the PARP inhibitor, e.g., organoids that experience at least a threshold level of cell death upon exposure of the organoid to the PARP inhibitor, and (ii) organoids, cultured from one or more cells of a respective tumor biopsy in the plurality of tumor biopsies, that have a second sensitivity to the PARP inhibitor, e.g., organoids that experience less than a threshold level of cell death upon exposure of the organoid to the PARP inhibitor.

In some embodiments, the classifier is further trained against, for each respective tissue sample in the plurality of tissue samples, one or more phenotypic characteristics of the tissue sample. In some embodiments, the one or more phenotypic characteristics of the tissue sample include a histologic feature of the tissue sample.

In some embodiments, the classifier is further trained against, for each respective tissue sample in the plurality of tissue samples, one or more characteristics of the subject from which the tissue sample was obtained, e.g., as described above.

In some embodiments, the classifier is a multinomial classifier that is trained to provide a plurality of likelihoods, wherein each respective likelihood in the plurality of likelihoods is a likelihood that tumor cells from a test subject with cancer will have a different respective sensitivity in the two or more tumor sensitivities to a PARP inhibitor. In some embodiments, the classifier is a neural network algorithm, a support vector machine algorithm, a Naive Bayes algorithm, a nearest neighbor algorithm, a boosted trees algorithm, a random forest algorithm, a convolutional neural network algorithm, a decision tree algorithm, a regression algorithm, or a clustering algorithm.

Diagnosing PARPi Sensitivity

In some embodiments, the disclosure provides method and systems for performing methods of recommending therapy for treating a cancer in a subject. In some embodiments, the method includes obtaining a first test data set comprising a plurality of nucleic acid features of a tumor biopsy from the test subject. The method then includes evaluating the first test data set using a classifier trained to discriminate between two or more tumor sensitivities to a first poly ADP ribose polymerase (PARP) inhibitor. The classifier is trained against, for each respective training tissue sample in a plurality of training tissue samples, at least (i) the plurality of nucleic acid features obtained from the respective training tissue sample, and (ii) a corresponding indication of the sensitivity of a respective organoid cultured from one or more cells of the respective training tissue sample to the first PARP inhibitor. In some embodiments, the sensitivity of the training tissue sample is determined in a two-dimensional cell culture, a three-dimensional cell culture prepared in a matrix, a three-dimensional cell culture prepared in suspension culture, a cell culture suspension, or a xenograft model. A first tumor sensitivity in the two or more tumor sensitivities to the first PARP inhibitor is associated with a first recommendation, in a plurality of recommendations, to treat the cancer in the subject with the first PARP inhibitor. A second tumor sensitivity in the two or more tumor sensitivities to the first PARP inhibitor is associated with a second recommendation, in the plurality of recommendations, not to treat the cancer in the subject with the first PARP inhibitor. In some embodiments, the method includes providing a respective recommendation, in the plurality of recommendations, for treating the cancer in the test subject based on the results of the evaluation.

In some embodiments, the cancer is a breast cancer. In some embodiments, the cancer is an ovarian cancer. In some embodiments, the cancer is not breast cancer or ovarian cancer. In some embodiments, the test subject has not previously been treated for cancer. That is, in some embodiments, the PARP inhibitor is administered as a first-line therapy. In some embodiments, the test subject has been previously treated for the cancer. That is, in some embodiments, the PARP inhibitor is administered as a second-line therapy. In some embodiments, the PARP inhibitor is olaparib, veliparib, rucaparib, niraparib, or talazoparib.

In some embodiments, the plurality of nucleic acid features of the tumor biopsy comprise one or more of support for a single nucleotide variant at a genomic location, a methylation status at a genomic location, a relative copy number for a genomic location, an allelic ratio for a genomic location, a relative expression level of a gene, and mathematical combinations thereof. In some embodiments, the plurality of nucleic acid features of the tumor biopsy comprises a BRCA1 or BRCA2 mutant allele status.

In some embodiments, the first test data set further comprises a cancer status of the test subject in a plurality of cancer statuses, the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, a cancer status of the respective training tissue sample in the plurality of cancer statuses.

In some embodiments, the plurality of cancer statuses comprises a plurality of types of cancer. In some embodiments, the plurality of cancer statuses comprises a plurality of stages of cancer.

In some embodiments, the first test data set further comprises one or more phenotypic characteristics of the tumor biopsy, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, the one or more phenotypic characteristics of the respective training tissue sample. In some embodiments, the one or more phenotypic characteristics of the tumor biopsy comprise a histologic feature of the tumor biopsy.

In some embodiments, the first test data set further comprises one or more characteristics of the subject, as described in the feature selection section above, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, the one or more characteristics of the subject from which the respective training tissue sample was obtained.

In some embodiments, the method also includes obtaining a second test data set comprising the plurality of nucleic acid features of a tumor biopsy from the test subject, and evaluating the second test data set using the classifier trained to discriminate between two or more tumor sensitivities to a first poly ADP ribose polymerase (PARP) inhibitor, where the plurality of nucleic acid features in the first test data set are from a first tumor biopsy from the test subject and the second test data set are from a second tumor biopsy from the test subject that is different from the first tumor biopsy. In some embodiments, the first tumor biopsy and the second tumor biopsy are from different sections of a same tumor of the subject. In some embodiments, the first tumor biopsy and the second tumor biopsy are from different tumors of the subject.

In some embodiments, the classifier is a multinomial classifier that is trained to provide a plurality of likelihoods, wherein each respective likelihood in the plurality of likelihoods is a likelihood that a different respective treatment regime, in a plurality of treatment regimes, for the cancer in the subject will be more effective than the other treatment regimes in the plurality of treatment regimes.

In some embodiments, the classifier is a neural network algorithm, a support vector machine algorithm, a Naive Bayes algorithm, a nearest neighbor algorithm, a boosted trees algorithm, a random forest algorithm, a convolutional neural network algorithm, a decision tree algorithm, a regression algorithm, or a clustering algorithm.

In some embodiments, first PARP inhibitor is selected from the group consisting of olaparib, veliparib, rucaparib, niraparib, and talazoparib. In some embodiments, the classifier is trained to further discriminate between two or more tumor sensitivities to a second PARP inhibitor, wherein the second PARP inhibitor is different than the first PARP inhibitor. In some embodiments, the second PARP inhibitor is selected from the group consisting of olaparib, veliparib, rucaparib, niraparib, and talazoparib. In some embodiments, the classifier is trained to further discriminate between two or more tumor sensitivities to a chemotherapeutic drug that is not a PARP inhibitor.

In some embodiments, the first recommendation is a recommendation to treat the cancer in the subject with the first PARP inhibitor as a first-line therapy. In some embodiments, the first recommendation is a recommendation to treat the cancer in the subject with the first PARP inhibitor as a second-line therapy.

In some embodiments, the first recommendation is a recommendation to treat the cancer in the subject with the first PARP inhibitor and without any other chemotherapeutic drug. In some embodiments, after providing, or instead of providing, the first recommendation for treating the cancer in the subject, the method includes administering the first PARP inhibitor to the test subject.

In some embodiments, the first recommendation is a recommendation to treat the cancer in the subject with the first PARP inhibitor and with a second cancer therapy, e.g., radiation, surgery, a second PARP inhibitor, or a chemotherapeutic drug that is not a PARP inhibitor. In some embodiments, after providing, or instead of providing, the first recommendation for treating the cancer in the subject, the method includes co-administering the first PARP inhibitor and the second cancer therapy to the test subj ect. In some embodiments, the second cancer therapy is administration of a chemotherapeutic drug that is not a PARP inhibitor.

In some embodiments, the second recommendation is a recommendation to treat the cancer in the subject with a second PARP inhibitor. In some embodiments, after providing, or instead of providing, the second recommendation for treating the cancer in the subject, the method includes administering the second PARP inhibitor to the test subject.

In some embodiments, the plurality of recommendations further comprises a third recommendation to treat the cancer in the subject with a chemotherapeutic drug that is not a PARP inhibitor. In some embodiments, after providing, or instead of providing, the third recommendation for treating the cancer in the subject, the method includes administering the chemotherapeutic drug that is not a PARP inhibitor to the test subject.

In some embodiments, the second recommendation is a recommendation to treat the cancer in the subject with a therapeutic drug that is not a PARP inhibitor. In some embodiments, after providing, or instead of providing, the second recommendation for treating the cancer in the subject, the method includes administering the chemotherapeutic drug that is not a PARP inhibitor to the test subject.

In some embodiments, the first recommendation is a recommendation to treat the cancer in the subject with the first PARP inhibitor at a first therapeutic dose, and the plurality of recommendations further comprises a fourth recommendation to treat the cancer in the subject with the first PARP inhibitor at a second therapeutic dose.

In some embodiments, prior to providing the respective recommendation, the method includes identifying at least two recommendations, in the plurality of recommendations, based on the results of the evaluation, e.g., that are associated with better likelihoods that their associated treatment regimens will be more effective than treatment regimens associated with other recommendations, and determining a sensitivity of the cancer in the subject to each respective therapy regimen, in a plurality of therapy regimens, associated with the at least two recommendations by: a) culturing a plurality of tumor organoids, each respective tumor organoid in the plurality of tumor organoids from one or more cells of a tumor biopsy from the subject, b) exposing the one or more organoids cultured in a) to one or more amounts of a therapeutic agent associated with the respective therapy regimen, and c) measuring the fitness of cells, e.g., using a cellular viability assay or cell death assay, in the one or more organoids following the exposure to the one or more amounts of the therapeutic agent, thereby obtaining one or more cellular fitness measurements for each respective therapy regimen associated with the two or more recommendations. In this embodiments, the therapeutic recommendation and/or treatment is selected from the two or more recommendations and is based on the one or more cellular fitness measurements obtained for each respective therapy regimen associated with the two or more recommendations.

In some embodiments, the methods described herein include administering the recommended therapy for treating cancer to the test subject.

Treatment of BRCA1-/2-cancers with PARPi

In some embodiments, the disclosure provides methods and systems for performing methods of treating a cancer other than breast cancer or ovarian cancer in a test subject. In some embodiments, the methods include determining a probability or likelihood that the cancer will be sensitive to a poly ADP ribose polymerase (PARP) inhibitor, and treating cancer in the subject. When the probability or likelihood that the cancer will be sensitive to the PARP inhibitor satisfies a threshold likelihood, the method includes administering, or communicating, a recommended therapy comprising the PARP inhibitor to the test subject. When the probability or likelihood that the cancer will be sensitive to the PARP inhibitor does not satisfy a threshold likelihood, the method includes administrating, or communicating, a recommended therapy that does not include the PARP inhibitor to the test subject.

In some embodiments, the cancer is a breast cancer. In some embodiments, the cancer is an ovarian cancer. In some embodiments, the cancer is not breast cancer or ovarian cancer. In some embodiments, the test subject has not previously been treated for cancer. That is, in some embodiments, the PARP inhibitor is administered as a first-line therapy. In some embodiments, the test subject has been previously treated for the cancer. That is, in some embodiments, the PARP inhibitor is administered as a second-line therapy. In some embodiments, the PARP inhibitor is olaparib, veliparib, rucaparib, niraparib, or talazoparib.

In some embodiments, the probability or likelihood that the cancer will be sensitive to the PARP inhibitor is determined by: 1) culturing a plurality of tumor organoids, each respective tumor organoid in the plurality of tumor organoids from one or more cells of a tumor biopsy from the test subject, 2) exposing the one or more organoids cultured in a) to one or more amounts of the PARP inhibitor, 3) measuring the fitness of cells, e.g., using a cellular viability assay or cell death assay, in the one or more tumor organoids following the exposure to the one or more amounts of the PARP inhibitor, and 4) correlating the measured fitness of the cells with a probability or likelihood that the cancer will be sensitive to the PARP inhibitor.

In some embodiments, the probability or likelihood that the cancer will be sensitive to the PARP inhibitor is determined by: 1) obtaining a first test data set comprising a plurality of nucleic acid features of a tumor biopsy from the test subject, 2) evaluating the first test data set using a classifier trained to discriminate between two or more tumor sensitivities to the PARP inhibitor, where the classifier was trained against, for each respective training tissue sample in a plurality of training tissue samples, at least (i) the plurality of nucleic acid features obtained from the respective training tissue sample, and (ii) a corresponding indication of the sensitivity of a respective organoid cultured from one or more cells of the respective training tissue sample to the PARP inhibitor.

In some embodiments, the plurality of nucleic acid features of the tumor biopsy comprise one or more of support for a single nucleotide variant at a genomic location, a methylation status at a genomic location, a relative copy number for a genomic location, an allelic ratio for a genomic location, a relative expression level of a gene, and mathematical combinations thereof.

In some embodiments, the first test data set further comprises a cancer status of the test subject in a plurality of cancer statuses, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, a cancer status of the respective training tissue sample in the plurality of cancer statuses. In some embodiments, the plurality of cancer statuses comprises a plurality of types of cancer. In some embodiments, the plurality of cancer statuses comprises a plurality of stages of cancer.

In some embodiments, the first test data set further comprises one or more phenotypic characteristics of the tumor biopsy, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, the one or more phenotypic characteristics of the respective training tissue sample. In some embodiments, the one or more phenotypic characteristics of the tumor biopsy comprise a histologic feature of the tumor biopsy.

In some embodiments, the first test data set further comprises one or more characteristics of the subject, as described in the feature selection section above, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, the one or more characteristics of the subject from which the respective training tissue sample was obtained.

In some embodiments, the method also includes obtaining a second test data set comprising the plurality of nucleic acid features of a tumor biopsy from the test subject, and evaluating the second test data set using the classifier trained to discriminate between the two or more tumor sensitivities to the PARP inhibitor, where the plurality of nucleic acid features in the first test data set are from a first tumor biopsy from the test subject and the second test data set are from a second tumor biopsy from the test subject that is different from the first tumor biopsy. Ins some embodiments, the first tumor biopsy and the second tumor biopsy are from different sections of a same tumor of the subject. In some embodiments, the first tumor biopsy and the second tumor biopsy are from different tumors of the subject.

In some embodiments, the classifier is a multinomial classifier that is trained to provide a plurality of likelihoods, wherein each respective likelihood in the plurality of likelihoods is a likelihood that a different respective treatment regime, in a plurality of treatment regimes, for the cancer in the subject will be more effective than the other treatment regimes in the plurality of treatment regimes.

In some embodiments, the classifier is a neural network algorithm, a support vector machine algorithm, a Naive Bayes algorithm, a nearest neighbor algorithm, a boosted trees algorithm, a random forest algorithm, a convolutional neural network algorithm, a decision tree algorithm, a regression algorithm, or a clustering algorithm.

In some embodiments, the methods described herein also include administering the recommended therapy for treating cancer to the test subject.

Treatment of Non-Breast/Ovarian Cancers with PARPi

In some embodiments, the disclosure provides methods and systems for performing methods of treating a cancer other than breast cancer or ovarian cancer in a test subject. In some embodiments, the methods include determining a probability or likelihood that the cancer will be sensitive to a poly ADP ribose polymerase (PARP) inhibitor, and treating cancer in the subject. When the probability or likelihood that the cancer will be sensitive to the PARP inhibitor satisfies a threshold likelihood, the method includes administering, or communicating, a recommended therapy comprising the PARP inhibitor to the test subject. When the probability or likelihood that the cancer will be sensitive to the PARP inhibitor does not satisfy a threshold likelihood, the method includes administrating, or communicating, a recommended therapy that does not include the PARP inhibitor to the test subject.

In some embodiments, the cancer is a BRCA1-/BRCA2-cancer. In some embodiments, the cancer is a colorectal cancer. In some embodiments, the cancer is a lung cancer. In some embodiments, the cancer is a non-small cell lung cancer. In some embodiments, the cancer is an endometrial cancer. In some embodiments, the test subject has not previously been treated for cancer. In some embodiments, the test subject has previously been treated for the cancer.

In some embodiments, the PARP inhibitor is selected from the group consisting of olaparib, veliparib, rucaparib, niraparib, and talazoparib.

In some embodiments, the probability or likelihood that the cancer will be sensitive to the PARP inhibitor is determined by: 1) culturing a plurality of tumor organoids, each respective tumor organoid in the plurality of tumor organoids from one or more cells of a tumor biopsy from the test subject, 2) exposing the one or more organoids cultured in a) to one or more amounts of the PARP inhibitor, 3) measuring the fitness of cells, e.g., using a cellular viability assay or cell death assay, in the one or more tumor organoids following the exposure to the one or more amounts of the PARP inhibitor, and 4) correlating the measured fitness of the cells with a probability or likelihood that the cancer will be sensitive to the PARP inhibitor.

In some embodiments, the probability or likelihood that the cancer will be sensitive to the PARP inhibitor is determined by: 1) obtaining a first test data set comprising a plurality of nucleic acid features of a tumor biopsy from the test subject, and 2) evaluating the first test data set using a classifier trained to discriminate between two or more tumor sensitivities to the PARP inhibitor, where the classifier was trained against, for each respective training tissue sample in a plurality of training tissue samples, at least (i) the plurality of nucleic acid features obtained from the respective training tissue sample, and (ii) a corresponding indication of the sensitivity of a respective organoid cultured from one or more cells of the respective training tissue sample to the PARP inhibitor.

In some embodiments, the plurality of nucleic acid features of the tumor biopsy are selected from the group consisting of support for a single nucleotide variant at a genomic location, a methylation status at a genomic location, a relative copy number for a genomic location, an allelic ratio for a genomic location, a relative expression level of a gene, and a mathematical combination thereof

In some embodiments, the first test data set further comprises a cancer status of the test subject in a plurality of cancer statuses, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, a cancer status of the respective training tissue sample in the plurality of cancer statuses. In some embodiments, the plurality of cancer statuses comprises a plurality of types of cancer. In some embodiments, the plurality of cancer statuses comprises a plurality of stages of cancer.

In some embodiments, the first test data set further comprises one or more phenotypic characteristics of the tumor biopsy, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, the one or more phenotypic characteristics of the respective training tissue sample. In some embodiments, the one or more phenotypic characteristics of the tumor biopsy comprise a histologic feature of the tumor biopsy.

In some embodiments, the first test data set further comprises one or more characteristics of the subject, as described in the feature selection section above, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, the one or more characteristics of the subject from which the respective training tissue sample was obtained.

In some embodiments, the method also includes obtaining a second test data set comprising the plurality of nucleic acid features of a tumor biopsy from the test subject, and evaluating the second test data set using the classifier trained to discriminate between the two or more tumor sensitivities to the PARP inhibitor, where the plurality of nucleic acid features in the first test data set are from a first tumor biopsy from the test subject and the second test data set are from a second tumor biopsy from the test subject that is different from the first tumor biopsy. In some embodiments, the first tumor biopsy and the second tumor biopsy are from different sections of a same tumor of the subject. In some embodiments, the first tumor biopsy and the second tumor biopsy are from different tumors of the subject.

In some embodiments, the classifier is a multinomial classifier that is trained to provide a plurality of likelihoods, wherein each respective likelihood in the plurality of likelihoods is a likelihood that a different respective treatment regime, in a plurality of treatment regimes, for the cancer in the subject will be more effective than the other treatment regimes in the plurality of treatment regimes.

In some embodiments, the classifier is a neural network algorithm, a support vector machine algorithm, a Naive Bayes algorithm, a nearest neighbor algorithm, a boosted trees algorithm, a random forest algorithm, a convolutional neural network algorithm, a decision tree algorithm, a regression algorithm, or a clustering algorithm.

In some embodiments, the methods described herein also include administering the recommended therapy for treating cancer to the test subject.

Providing PARPi info on a clinical report

In some embodiments, the disclosure provides methods and systems for performing methods of providing a clinical report for a cancer patient to a physician. In some embodiments, the methods include obtaining a first test data set comprising features of a transcriptome from a tumor biopsy from the cancer patient. In some embodiments, the methods include evaluating the first test data set using a classifier trained, e.g., as described herein, to discriminate between two or more tumor sensitivities to a first poly ADP ribose polymerase (PARP) inhibitor. The methods then include receiving a recommended therapy for the cancer patient from the classifier, and including the recommended therapy, or sending the recommended therapy to a third party for inclusion, in a clinical report for the cancer patient.

In some embodiments, the recommended therapy for the cancer patient comprises administration of the PARP inhibitor. In some embodiments, the PARP inhibitor is olaparib, veliparib, rucaparib, niraparib, or talazoparib.

In some embodiments, the patient has a BRCA1-/BRCA2-cancer. In some embodiments, the patient has a homologous recombination deficient (HRD) cancer. In some embodiments, the patient has a breast cancer. In some embodiments, the patient has an ovarian cancer. In some embodiments, the patient does not have has breast cancer or ovarian cancer. In some embodiments, the patient has a colorectal cancer. In some embodiments, the patient has a lung cancer. In some embodiments, the patient has a non-small cell lung cancer. In some embodiments, the patient has an endometrial cancer. In some embodiments, the patient has not previously been treated for cancer. In some embodiments, the patient has previously been treated for the cancer.

Research Tool for Identifying PARPi's

In some embodiments, the disclosure provides methods and systems for performing methods of identifying an inhibitor of poly ADP ribose polymerase (PARP). In some embodiments, the methods include obtaining a tissue sample that is sensitive to a known PARP inhibitor, and culturing one or more organoids, each respective organoid in the one or more organoids from one or more cells of the tissue sample. The methods then include exposing the one or more of the cultured organoids to one or more concentrations of a candidate molecule, and measuring the fitness of cells in the one or more organoids following the exposure to the one or more concentrations of the candidate molecule. A reduced fitness of cells in the one or more organoids is indicative that the candidate molecule is a PARP inhibitor.

In some embodiments, the PARP inhibitor is olaparib, veliparib, rucaparib, niraparib, or talazoparib.

In some embodiments, the tissue sample includes cells from a BRCA1-/BRCA2-cancer. In some embodiments, the tissue sample includes cells from a homologous recombination deficient (HRD) cancer. In some embodiments, the tissue sample includes cells from a breast cancer. In some embodiments, the tissue sample includes cells from an ovarian cancer. In some embodiments, the tissue sample does not includes cells from a breast cancer or ovarian cancer. In some embodiments, the tissue sample includes cells from a colorectal cancer.

In some embodiments, the tissue sample includes cells from a lung cancer. In some embodiments, the tissue sample includes cells from a non-small cell lung cancer. In some embodiments, the tissue sample includes cells from an endometrial cancer. In some embodiments, the tissue sample includes cells from a patient that has not previously been treated for cancer. In some embodiments, the tissue sample includes cells from a patient that has previously been treated for the cancer.

Research Tool for Repurposing Drugs

In some embodiments, the disclosure provides methods and systems for performing methods of identifying a new use for a pharmaceutical compound of a first pharmaceutical class. In some embodiments, the methods include obtaining a plurality of tissue samples, wherein each respective tissue sample in the plurality of tissue samples is sensitive to a respective class of pharmaceutical agents in a plurality of classes of pharmaceutical agents that excludes the first pharmaceutical class. The methods then includes culturing, for each respective tissue sample in the plurality of tissue samples, one or more respective organoids from one or more cells of the respective tissue sample, thereby generating a plurality of organoid cultures. The methods then include exposing, for each organoid culture in the plurality of organoid cultures, the respective one or more organoids to one or more concentrations of the pharmaceutical agent, and measuring, for each organoid culture in the plurality of organoid cultures, the fitness of cells in the respective one or more organoids following the exposure to the pharmaceutical agent. Reduced fitness of the cells in the respective one or more organoids is indicative that the pharmaceutical molecule shares pharmacological properties with the class of pharmaceutical compounds in the plurality of classes of pharmaceutical classes to which the tissue sample corresponding to the respective one or more organoids is sensitive.

In some embodiments, the plurality of tissue samples comprises cells from at least 3 different types of cancers. In some embodiments, the plurality of tissue samples comprises cells from at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more different types of cancers.

Selecting Patients for Clinical Trials with an Organoid Assay

In some embodiments, the disclosure provides methods and systems for performing methods of determining the eligibility of a cancer patient for a clinical trial of a candidate cancer pharmaceutical agent. In some embodiments, the methods include obtaining a tumor biopsy from the cancer patient, and culturing one or more tumor organoids from one or more cells of the tumor biopsy. The methods then include exposing the one or more tumor organoids to one or more concentrations of the candidate cancer pharmaceutical agent, and measuring the fitness of cells in the one or more tumor organoids following the exposure to the one or more concentrations of the candidate cancer pharmaceutical agent. The methods then include determining whether the cancer patient is eligible for the clinical trial based on at least the measured fitness of the cells in the one or more tumor organoids, wherein reduced fitness of the cells in the one or more tumor organoids is indicative that the cancer patient is eligible for the clinical trial. In some embodiments, the candidate cancer pharmaceutical agent is a poly ADP ribose polymerase (PARP) inhibitor.

In some embodiments, the clinical trial is for the treatment of a BRCA1-/BRCA2-cancer. In some embodiments, the clinical trial is for the treatment of a homologous recombination deficient (HRD) cancer. In some embodiments, the clinical trial is for the treatment of a breast cancer. In some embodiments, the clinical trial is for the treatment of an ovarian cancer. In some embodiments, the clinical trial is for the treatment of a breast cancer or ovarian cancer. In some embodiments, the clinical trial is for the treatment of a colorectal cancer. In some embodiments, the clinical trial is for the treatment of a lung cancer. In some embodiments, the clinical trial is for the treatment of a non-small cell lung cancer. In some embodiments, the clinical trial is for the treatment of an endometrial cancer. In some embodiments, the clinical trial is for the treatment of a patient that has not previously been treated for cancer. In some embodiments, the clinical trial is for the treatment of a patient that has previously been treated for the cancer.

Selecting Patients for Clinical Trials with a Classifier

In some embodiments, the disclosure provides methods and systems for performing methods of determining the eligibility of a cancer patient for a clinical trial of a candidate cancer pharmaceutical agent. In some embodiments, the methods include obtaining a first test data set comprising a plurality of nucleic acid features of a tumor biopsy from the cancer patient. The methods then include evaluating the first test data set using a classifier trained to discriminate between two or more tumor sensitivities to the candidate cancer pharmaceutical agent. The classifier is trained against, for each respective training tissue sample in a plurality of training tissue samples, at least (i) the plurality of nucleic acid features obtained from the respective training tissue sample, and (ii) a corresponding indication of the sensitivity of a respective organoid cultured from one or more cells of the respective training tissue sample to the candidate cancer pharmaceutical agent. A first tumor sensitivity in the two or more tumor sensitivities to the candidate cancer pharmaceutical agent is associated with an indication that the cancer patient is eligible for the clinical trial. A second tumor sensitivity in the two or more tumor sensitivities to the candidate cancer pharmaceutical agent is associated with an indication that the cancer patient is eligible for the clinical trial. The methods then include determining whether the cancer patient is eligible for the clinical trial based on at least the evaluation. In some embodiments, the candidate cancer pharmaceutical agent is a poly ADP ribose polymerase (PARP) inhibitor.

In some embodiments, the clinical trial is for the treatment of a BRCA1-/BRCA2-cancer. In some embodiments, the clinical trial is for the treatment of a homologous recombination deficient (HRD) cancer. In some embodiments, the clinical trial is for the treatment of a breast cancer. In some embodiments, the clinical trial is for the treatment of an ovarian cancer. In some embodiments, the clinical trial is for the treatment of a breast cancer or ovarian cancer. In some embodiments, the clinical trial is for the treatment of a colorectal cancer. In some embodiments, the clinical trial is for the treatment of a lung cancer. In some embodiments, the clinical trial is for the treatment of a non-small cell lung cancer. In some embodiments, the clinical trial is for the treatment of an endometrial cancer. In some embodiments, the clinical trial is for the treatment of a patient that has not previously been treated for cancer. In some embodiments, the clinical trial is for the treatment of a patient that has previously been treated for the cancer.

In some embodiments, the candidate cancer pharmaceutical agent has previously been found to be effective for the treatment of a cancer having a first clinical marker and the clinical trial is for the treatment of a cancer that does not have the first clinical marker.

In some embodiments, the plurality of nucleic acid features of the tumor biopsy include one or more of support for a single nucleotide variant at a genomic location, a methylation status at a genomic location, a relative copy number for a genomic location, an allelic ratio for a genomic location, a relative expression level of a gene, and a mathematical combination thereof.

In some embodiments, the first test data set also includes a cancer status of the test subject in a plurality of cancer statuses, and the classifier was further trained against, for each respective training tissue sample in a plurality of the training tissue samples, a cancer status of the respective training tissue sample in the plurality of cancer statuses. In some embodiments, the plurality of cancer statuses comprises a plurality of types of cancer. In some embodiments, the plurality of cancer statuses comprises a plurality of stages of cancer.

In some embodiments, the first test data set further comprises one or more phenotypic characteristics of the tumor biopsy, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, the one or more phenotypic characteristics of the respective training tissue sample. In some embodiments, the one or more phenotypic characteristics of the tumor biopsy comprise a histologic feature of the tumor biopsy.

In some embodiments, the first test data set also includes one or more characteristics of the subject, as described in the feature selection section above, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, the one or more characteristics of the subject from which the respective training tissue sample was obtained.

Detecting Drug Resistance with a Classifier

In some embodiments, the disclosure provides methods and systems for performing methods of identifying a resistance to a chemotherapeutic agent in a patient with cancer. In some embodiments, the methods include obtaining a first test data set comprising a plurality of nucleic acid features of a tumor biopsy from the patient with cancer. The methods then include evaluating the first test data set using a classifier trained to discriminate between two or more tumor sensitivities to the chemotherapeutic agent. The classifier is trained against, for each respective training tissue sample in a plurality of training tissue samples, at least (i) the plurality of nucleic acid features obtained from the respective training tissue sample, and (ii) a corresponding indication of the sensitivity of a respective organoid cultured from one or more cells of the respective training tissue sample to the chemotherapeutic agent. A first tumor sensitivity in the two or more tumor sensitivities to the candidate cancer pharmaceutical agent is associated with an indication that the patient's cancer is resistant to the chemotherapeutic agent.

A second tumor sensitivity in the two or more tumor sensitivities to the candidate cancer pharmaceutical agent is associated with an indication that the patient's cancer is not resistant to the chemotherapeutic agent. The methods then include providing a report indicating whether the patient's cancer is resistant to the chemotherapeutic agent based on at least the results of the evaluation.

In some embodiments, chemotherapeutic agent is a PARP inhibitor. In some embodiments, the PARP inhibitor is olaparib, veliparib, rucaparib, niraparib, or talazoparib.

In some embodiments, the patient has a BRCA1-BRCA2-cancer. In some embodiments, the patient has a cancer that carries a BRCA1 or BRCA2 mutation. In some embodiments, the patient has a homologous recombination deficient (HRD) cancer. In some embodiments, the patient has a breast cancer. In some embodiments, the patient has an ovarian cancer. In some embodiments, the patient does not have has breast cancer or ovarian cancer. In some embodiments, the patient has a colorectal cancer. In some embodiments, the patient has a lung cancer. In some embodiments, the patient has a non-small cell lung cancer. In some embodiments, the patient has an endometrial cancer. In some embodiments, the patient has not previously been treated for cancer. In some embodiments, the patient has previously been treated for the cancer.

In some embodiments, the chemotherapeutic agent has been previously associated with a clinical marker and the cancer has the clinical marker.

In some embodiments, the plurality of nucleic acid features includes one or more of support for a single nucleotide variant at a genomic location, a methylation status at a genomic location, a relative copy number for a genomic location, an allelic ratio for a genomic location, a relative expression level of a gene, and a mathematical combination thereof. In some embodiments, the plurality of nucleic acid features comprises a BRCA1 or BRCA2 mutant allele status.

In some embodiments, the first test data set also includes one or more phenotypic characteristics of the tumor biopsy, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, the one or more phenotypic characteristics of the respective training tissue sample. In some embodiments, the one or more phenotypic characteristics of the tumor biopsy comprise a histologic feature of the tumor biopsy.

In some embodiments, the first test data set also includes one or more characteristics of the subject, as described in the feature selection section above, and the classifier was further trained against, for each respective training tissue sample in a plurality of training tissue samples, the one or more characteristics of the subject from which the respective training tissue sample was obtained.

Evaluating Effect of Cancer Drug Using Tumor Organoid Assay and Assigning Cancer Treatment Based on Tumor Organoid Assay

In some aspects, the present disclosure provides systems and methods for large scale analysis of therapeutic responses using tumor organoids (TOs).

In certain aspects, a drug screening platform may be utilized to assess the effectiveness of drugs or other agents on tumor organoids. In one embodiment, tumor organoids are first dissociated into single cells, which are then seeded into individual partitions in the presence of tumor organoid culture media. Tumor organoids used in the methods provided herein can be derived from cells from any suitable cancer including, but not limited to, an anal cancer, a basal cell skin cancer, a squamous cancer, a breast cancer, a bladder cancer, a cervical cancer, a colon cancer, an endometrial cancer, a head and neck cancer, a hepatobiliary cancer, a kidney cancer, a gastric cancer, a lung cancer, a mesothelial cancer of the pleural cavity, a mesothelial cancer of the peritoneal cavity, an ovarian cancer, prostate cancer, a rectal cancer.

Tumor organoids that subsequently form from the individual cells in each partition exhibit tumor organoid heterogeneity. In some embodiments, the single cells are seeded in a multi-well plate (e.g., 24-, 48-, 96-, 384-well). Preferably, individual cells are seeded at a density to allow sufficient number of TOs to form while not overcrowding the plate so that TOs do not overlap or touch allowing for easy identification of individual TOs.

Any suitable tumor organoid medium can be used to culture the tumor organoids. In some embodiments, the tumor organoid medium includes one or more tumor organoid growth factors. Organoid growth factors include an epidermal growth factor (EGF), a fibroblast growth factor (FGF), a hepatocyte growth factor (HGF), a Wnt, Noggin, an R-spondin, Gastrin, Prostaglandin, and Neuregulin. Organoid growth factors include ligands (natural, semi-synthetic, or synthetic, agonist or antagonist) of EGF family receptors, HGF family of receptors, Wnt family receptors, NOTCH family receptors, LRP receptor, Frizzled receptor, LGR5 receptor, insulin receptor, neuregulin family of receptors, or any growth factor receptor tyrosine kinase family member. Exemplary organoid culture media are summarized below in Table 1. In particular embodiments, the organoid culture medium is free of R-spondins. In some embodiments, the organoid culture medium is free of Wnt.

TABLE 1 Organoid Culture Molecular Medium Growth Factors Inhibitors Additional Components B Noggin Rho kinase a chemically-defined, minimal inhibitor, culture medium; L-glutamine; a transforming serum replacement supplement; growth factor-beta N-acetyl-L-cysteine; and inhibitor, and nicotinamide MAP kinase inhibitor C EGF and Noggin Rho kinase a chemically-defined, minimal inhibitor, culture medium; L-glutamine; a transforming serum replacement supplement; growth factor-beta N-acetyl-L-cysteine; and inhibitor, and nicotinamide MAP kinase inhibitor D EGF, Noggin, Rho kinase a chemically-defined, minimal FGF7 and inhibitor, culture medium; L-glutamine; a FGF10 transforming serum replacement supplement; growth factor-beta N-acetyl-L-cysteine; and inhibitor, and nicotinamide MAP kinase inhibitor

In one example, the TOs are also cultured in the presence of one or more extracellular matrix (ECM) components that function as a substrate for culturing the TO. In particular embodiments, the substrate is a Matrigel.

In one example, one or more agents (e.g., a therapeutic agent) are applied to the TOs in the partitions. Exemplary therapeutic agents include, but are not limited to, a molecular inhibitors, antibodies, recombinant nucleic acids (e.g., antisense oligonucleotides) and engineered immune cells (e.g., CAR T-cells and NK cells). Exemplary therapeutic agents include, but are not limited to, Paclitaxel, Gemcitabine, Cisplatin, Carboplatin, Oxaliplatin, Capecitabine, SN-38 (CPT-11), 5-FU, MTX (methotrexate), Docetaxel, Bortezomib, Everolimus, Ulixertinib, Dasatinib, Vinblastine, Nelarabine, Epirubicin, Afatinib, Lapatinib, Cytarabine, Cladribine, Doxorubicin, Azacitidine, and Staurosporine. Other examples include classes of drugs including but not limited to: taxanes, platinating agents, vinca alkaloids, alkylating agents, and anthracyclines. One or more molecular inhibitors may be applied to the TOs in the well plates. Molecular inhibitors may be selected by name, target, pathway, formula, or other known characterizations. Additional exemplary therapeutic agents that can be used with the methods described herein are provided in Table 2.

TABLE 2 Agent Target Pathway Formula Veliparib (ABT-888) PARP DNA Damage C₁₃H₁₆N₄O Selumetinib (AZD6244) MEK MAPK C₁₇H₁₅BrClFN₄O₃ PD184352 (CI-1040) MEK MAPK C₁₇H₁₄ClF₂IN₂O₂ PD0325901 MEK MAPK C₁₆H₁₄F₃IN₂O₄ Tozasertib (VX-680, Aurora Kinase Cell Cycle C₂₃H₂₈N₈OS MK-0457) Y-27632 2HCl Autophagy, ROCK Cell Cycle C₁₄H₂₃C_(l2)N₃O Olaparib (AZD2281, PARP DNA Damage C₂₄H₂₃FN₄O₃ Ku-0059436) SL-327 MEK MAPK C₁₆H₁₂F₃N₃S SB431542 TGF-beta/Smad TGF-beta/Smad C₂₂H₁₆N₄O₃ MK-2206 2HCl Akt PI3K/Akt/mTOR C₂₅H₂₃C_(l2)N₅O Refametinib (RDEA119, Bay MEK MAPK C₁₉H₂₀F₃IN₂O₅S 86-9766) KU-55933 (ATM Kinase ATM/ATR DNA Damage C₂₁H₁₇NO₃S₂ Inhibitor) GSK1904529A IGF-1R Protein Tyrosine C₄₄H₄₇F₂N₉O₅S Kinase PF-04217903 c-Met Protein Tyrosine C₁₉H₁₆N₈O Kinase U0126-EtOH MEK MAPK C₂₀H₂₂N₆OS₂ BI 2536 PLK Cell Cycle C28H39N7O3 JNJ-38877605 c-Met Protein Tyrosine C19H13F2N7 Kinase Odanacatib (MK-0822) Cysteine Protease Proteases C₂₅H₂₇F₄N₃O₃S Alisertib (MLN8237) Aurora Kinase Cell Cycle C27H20ClFN4O4 Barasertib (AZD1152- Aurora Kinase Cell Cycle C26H30FN7O3 HQPA) CP-724714 EGFR, HER2 Protein Tyrosine C27H27N5O3 Kinase TGX-221 PI3K PI3K/Akt/mTOR C21H24N4O2 WZ4002 EGFR Protein Tyrosine C25H27ClN6O3 Kinase BIBR 1532 Telomerase DNA Damage C21H17NO3 Anastrozole Aromatase Endocrinology & C17H19N5 Hormones Aprepitant Substance P Others C23H21F7N4O3 TAK-700 (Orteronel) P450 (e.g. CYP17) Metabolism C18H17N3O2 PFI-1 (PF-6405761) Epigenetic Reader Epigenetics C16H17N3O4S Domain KU-0063794 mTOR PI3K/Akt/mTOR C25H31N5O4 CHIR-99021 (CT99021) GSK-3 PI3K/Akt/mTOR C22H18Cl2N8 WYE-354 mTOR PI3K/Akt/mTOR C24H29N7O5 TG100-115 PI3K PI3K/Akt/mTOR C18H14N6O2 Aurora A Inhibitor I Aurora Kinase Cell Cycle C31H31ClFN7O2 Ispinesib (SB-715992) Kinesin Cytoskeletal C30H33ClN4O2 Signaling Zibotentan (ZD4054) Endothelin Receptor GPCR & G C19H16N6O4S Protein Safinamide Mesylate MAO Metabolism C18H23FN2O5S GSK429286A ROCK Cell Cycle C21H16F4N4O2 Pimasertib (AS-703026) MEK MAPK C15H15FIN3O3 Tadalafil PDE Metabolism C22H19N3O4 Adavosertib (MK-1775) Wee1 Cell Cycle C27H32N8O2 CP-673451 PDGFR Protein Tyrosine C24H27N5O2 Kinase Selisistat (EX 527) Sirtuin Epigenetics C13H13ClN2O Dapagliflozin SGLT GPCR & G C21H25ClO6 Protein Nebivolol HCl Adrenergic Receptor Neuronal C22H26ClF2NO4 Signaling Pimobendan PDE Metabolism C19H18N4O2 AZD8055 mTOR PI3K/Akt/mTOR C25H31N5O4 KU-60019 ATM/ATR DNA Damage C30H33N3O5S Tie2 kinase inhibitor Tie-2 ProteinTyrosine C26H21N3O2S Kinase Apixaban Factor Xa Metabolism C25H25N5O4 Raltegravir (MK-0518) Integrase Microbiology C20H21FN6O5 PCI-34051 HDAC Epigenetics C17H16N2O3 Ambrisentan Endothelin Receptor GPCR & G C22H22N2O4 Protein SB743921 HCl Kinesin Cytoskeletal C31H34Cl2N2O3 Signaling AST-1306 EGFR Protein Tyrosine C₃₁H₂₆ClFN₄O₅S Kinase Sapitinib (AZD8931) EGFR, HER2 Protein Tyrosine C23H25ClFN5O3 Kinase GSK461364 PLK Cell Cycle C27H28F3N5O2S Mubritinib (TAK 165) HER2 Protein Tyrosine C25H23F3N4O2 Kinase UK 383367 Procollagen C Metabolism C15H24N4O4 Proteinase Cryptotanshinone STAT JAK/STAT C19H20O3 Icariin PDE Metabolism C33H40O15 OSI-027 mTOR PI3K/Akt/mTOR C21H22N6O3 Rabusertib (LY2603618) Chk Cell Cycle C18H22BrN5O3 URB597 FAAH Metabolism C20H22N2O3 A66 PI3K PI3K/Akt/mTOR C17H23N5O2S2 ICG-001 Wnt/beta-catenin Stem Cells & C33H32N4O4 Wnt PF-3845 FAAH Metabolism C24H23F3N4O2 Trametinib (GSK1120212) MEK MAPK C26H23FIN5O4 Ibrutinib (PCI-32765) BTK Angiogenesis C25H24N6O2 CHIR-124 Chk Cell Cycle C23H22ClN5O Mardepodect (PF-2545920) PDE Metabolism C25H20N4O WAY-600 mTOR PI3K/Akt/mTOR C28H30N8O Nepicastat (SYN-117) HCl Hydroxylase Metabolism C14H16ClF2N3S RS-127445 5-HT Receptor Neuronal C17H16FN3 Signaling CP-91149 Phosphorylase Metabolism C21H22ClN3O3 SB415286 GSK-3 PI3K/Akt/mTOR C16H10ClN3O5 GSK1070916 Aurora Kinase Cell Cycle C30H33N7O Niraparib (MK-4827) PARP DNA Damage C19H20N4O CHIR-98014 GSK-3 PI3K/Akt/mTOR C20H17Cl2N9O2 AMG-458 c-Met Protein Tyrosine C30H29N5O5 Kinase Tivantinib (ARQ 197) c-Met Protein Tyrosine C23H19N3O2 Kinase Canagliflozin SGLT GPCR & G C24H25FO5S Protein NVP-BVU972 c-Met Protein Tyrosine C20H16N6 Kinase MK-5108 (VX-689) Aurora Kinase Cell Cycle C₂₂H₂₁ClFN₃O₃S SB705498 TRPV Others C17H16BrF3N4O Vistusertib (AZD2014) mTOR PI3K/Akt/mTOR C25H30N6O3 A-803467 Sodium Channel Transmembrane C19H16ClNO4 Transporters Sirtinol Sirtuin Epigenetics C26H22N2O2 Ipatasertib (GDC-0068) Akt PI3K/Akt/mTOR C24H32ClN5O2 Sapanisertib (INK 128, mTOR PI3K/Akt/mTOR C15H15N7O MLN0128) Tyrphostin AG 879 HER2 Protein Tyrosine C18H24N2OS Kinase JNJ-1661010 FAAH Metabolism C19H19N5OS CTEP (RO4956371) GluR Neuronal C19H13ClF3N3O Signaling Alogliptin (SYK-322) DPP-4 Proteases C18H21N5O2 benzoate T0070907 PPAR DNA Damage C12H8ClN3O3 GW441756 Trk receptor Protein Tyrosine C17H13N3O Kinase SB742457 5-HT Receptor Neuronal C19H19N3O2S Signaling ZM 323881 HCl VEGFR Protein Tyrosine C22H19ClFN3O2 Kinase GNF-2 Bcr-Abl Angiogenesis C18H13F3N4O2 Lumiracoxib COX Neuronal C15H13ClFNO2 Signaling JNJ-7777120 Histamine Receptor Neuronal C14H16ClN3O Signaling IOX2 HIF Angiogenesis C19H16N2O5 PF-4981517 P450 (e.g. CYP17) Metabolism C26H32N8 CHIR-99021 (CT99021) HCl GSK-3 PI3K/Akt/mTOR C22H19Cl3N8 Rivaroxaban Factor Xa Metabolism C19H18ClN3O5S Linagliptin DPP-4 Proteases C25H28N8O2 Azilsartan Medoxomil RAAS Endocrinology & C30H24N4O8 Hormones Sulfaphenazole P450 (e.g. CYP17) Metabolism C15H14N4O2S Sitagliptin phosphate DPP-4 Proteases C16H20F6N5O6P monohydrate Avanafil PDE Metabolism C23H26ClN7O3 Eprosartan Mesylate RAAS Endocrinology & C24H28N2O7S2 Hormones Carprofen COX Neuronal C15H12ClNO2 Signaling Saxagliptin hydrate DPP-4 Proteases C18H27N3O3 Daminozide Histone Demethylase Epigenetics C6H12N2O3 Bedaquiline fumarate Anti-infection Microbiology C36H35BrN2O6 JZL184 Lipase Metabolism C27H24N2O9 SC-514 IκB/IKK NF-κB C9H8N2OS2 (R)-Nepicastat HCl Hydroxylase Metabolism C14H16ClF2N3S Asunaprevir HCV Protease Proteases C35H46ClN5O9S Trelagliptin succinate DPP-4 Proteases C22H26FN5O6 Dabrafenib Mesylate Raf MAPK C₂₄H₂₄F₃N₅O₅S₃ Argatroban Monohydrate Thrombin Others C23H38N6O6S Sitagliptin DPP-4 Proteases C16H15F6N5O Raltegravir potassium Integrase, HIV Microbiology C20H20FKN6O5 Protease Alogliptin DPP-4 Proteases C18H21N5O2 Dasabuvir(ABT-333) HCV Protease Proteases C26H27N3O5S Ertugliflozin SGLT2 Ion-Channel C22H25ClO7 Rolapitant NK1-receptor GPCR C25H26F6N2O2 Dapagliflozin propanediol SGLT GPCR & G C24H35ClO9 monohydrate Protein Bedaquiline tuberculosis Immunology C32H31BrN2O2 Fruquintinib VEGFRs VEGFR C21H19N3O5 JNJ0966 Others Others C16H16N4O2S2 acalisib (GS-9820) PI3K PI3K/Akt/mTOR C21H16FN7O BRL-50481 PDE Metabolism C9H12N2O4S Canagliflozin hemihydrate SGLT GPCR & G C48H52F2O11S2 Protein JANEX-1 JAK JAK/STAT C16H15N3O3 Anagliptin DPP-4 Proteases C19H25N7O2 GSK 5959 Epigenetic Reader Do Epigenetics C22H26N4O3 Pitolisant hydrochloride Histamine Receptor Neuronal C17H27Cl2NO Signaling K 858 Kinesin Cytoskeletal C13H15N3O2S Signaling BAY-61-3606 Syk Angiogenesis C20H20Cl2N603 Stattic STAT JAK/STAT C8H5NO4S GSK2656157 PERK Apoptosis C23H21FN6O XL388 mTOR PI3K/Akt/mTOR C23H22FN3O4S LY2090314 GSK-3 PI3K/Akt/mTOR C28H25FN6O3 MK-8745 Aurora Kinase Cell Cycle C20H19ClFN5OS Tepotinib (EMD 1214063) c-Met Protein Tyrosine C29H28N6O2 Kinase SGC 0946 Histone Epigenetics C28H40BrN7O4 Methyltransferase GSK2334470 PDK PI3K/Akt/mTOR C25H34N8O IPA-3 PAR Cytoskeletal C20H14O2S2 Signaling VE-822 ATM/ATR PI3K/Akt/mT0R C24H25N5O3S (+)-JQ1 Epigenetic Reader Epigenetics C23H25ClN4O2S Domain PYR-41 E1 Activating Ubiquitin C17H13N3O7 TCID DUB Ubiquitin C9H2Cl4O2 DMH1 TGF-beta/Smad TGF-beta/Smad C24H20N4O ML347 TGF-beta/Smad, ALK TGF-beta/Smad C22H16N4O UNC1999 Histone Epigenetics C33H43N7O2 Methyltransferase SSR128129E FGFR Angiogenesis C18H15N2NaO4 Spebrutinib (CC-292, BTK Angiogenesis C22H22FN5O3 AVL-292) SKI II S1P Receptor GPCR & G C15H11ClN2OS Protein PF-543 S1P Receptor GPCR & G C27H31NO4S Protein CID755673 Serine/threonin Apoptosis C12H11NO3 kinase, CaMK 1-Azakenpaullone GSK-3 PI3K/Akt/mTOR C15H10BrN3O CNX-2006 EGFR Protein Tyrosine C26H27F4N7O2 Kinase Bisindolylmaleimide I PKC TGF-beta/Smad C25H24N4O2 (GF109203X) Thiamet G Others Others C9H16N2O4S Alvelestat (AZD9668) Serine Protease Proteases C24H20F3N5O4S RGFP966 HDAC Epigenetics C21H19FN4O UNC0642 Histone Epigenetics C29H44F2N6O2 Methyltransferase NVP-TNKS656 PARP DNA Damage C27H34N4O5 AGI-6780 Dehydrogenase Metabolism C₂₁H₁₈F₃N₃O₃S₂ Ro3280 PLK Cell Cycle C27H35F2N7O3 NMS-P937 (NMS1286937) PLK Cell Cycle C24H27F3N8O3 CNX-774 BTK Angiogenesis C26H22FN7O3 AZD1981 GPR Endocrinology & C19H17ClN2O3S Hormones SRPIN340 Others Others C18H18F3N3O 4μ8C Others Others C11H8O4 NMS-E973 HSP (e g. HSP90) Cytoskeletal C22H22N4O7 Signaling PFI-2 HCl Histone Epigenetics C23H25F4N3O3S Methyltransferase GSK2606414 PERK Apoptosis C24H20F3N5O IPI-3063 PI3K PI3K/Akt/mTOR C25H25N7O2 Atglistatin Lipase Metabolism C17H21N3O CGP 57380 MNK MAPK C11H9FN6 SB-3CT MMP Proteases C15H14O3S2 AR-A014418 GSK-3 PI3K/Akt/mTOR C12H12N4O4S NH125 CaMK Neuronal C27H45IN2 Signaling XEN445 Lipase Metabolism C18H17F3N2O3R LDC000067 CDK Cell Cycle C18H18N4O3S PI-1840 Proteasome Proteases C22H26N4O3 FTI 277 HCl Transferase Metabolism C₂₂H₃₀C_(l)N₃O₃S₂ Nexturastat A HDAC DNA Damage C19H23N3O3 ESI-09 cAMP GPCR & G C16H15ClN4O2 Protein HJC0350 cAMP GPCR & G C15H19NO2S Protein HO-3867 STAT JAK/STAT C28H30F2N2O2 JNK Inhibitor IX JNK MAPK C20H16N2OS Trelagliptin DPP-4 Proteases C18H20FN5O2 XMD8-92 ERK MAPK C26H30N6O3 A-366 Histone Epigenetics C19H27N3O2 Methyltransferase GSK-LSD1 2HCl Histone Demethylase Epigenetics C14H22Cl2N2 LLY-507 Histone Epigenetics C36H42N6O Methyltransferase Santacruzamate A HDAC DNA Damage C15H22N2O3 (CAY10683) CAY10603 HDAC DNA Damage C22H30N4O6 GSK1324726A (I-BET726) Epigenetic Reader Epigenetics C25H23ClN2O3 Domain SD-208 TGF-beta/Smad TGF-beta/Smad C17H10ClFN6 TH588 MTH1 DNA Damage C13H12Cl2N4 SB225002 CXCR GPCR & G C13H10BrN3O4 Protein CPI-360 Histone Epigenetics C25H31N3O4 Methyltransferase Picropodophyllin (PPP) IGF-1R Protein Tyrosine C22H22O8 Kinase Savolitinib(AZD6094, c-Met Protein Tyrosine C17H15N9 HMPL-504) Kinase SP2509 Histone Demethylase Epigenetics C19H20ClN3O5S VX-11e ERK MAPK C₂₄H₂₀C_(l2)FN₅O₂ SBE 13 HCl PLK Cell Cycle C24H28Cl2N2O4 BLZ945 CSF-1R Protein Tyrosine C20H22N4O3S Kinase LFM-A13 BTK Angiogenesis C11H8Br2N2O2 EPZ015666(GSK3235025) Histone Epigenetics C20H25N5O3 Methyltransferase VER155008 HSP (e.g. HSP90) Cytoskeletal C25H23Cl2N7O4 Signaling BPTES Glutaminase Proteases C24H24N6O2S3 AZ6102 PPAR DNA Damage C25H28N6O Erlotinib EGFR Protein Tyrosine C22H23N3O4 Kinase ORY-1001 (RG-6016) 2HCl Histone Demethylase Epigenetics C15H24Cl2N2 EPZ020411 2HCl Histone Epigenetics C25H40Cl2N4O3 Methyltransferase I-BRD9 Epigenetic Reader Epigenetics C₂₂H₂₂F₃N₃O₃S₂ Domain SirReal2 Sirtuin Epigenetics C22H20N4OS2 BDA-366 Bcl-2 Apoptosis C24H29N3O4 NVP-CGM097 Mdm2 Apoptosis C38H47ClN4O4 CC-223 mTOR PI3K/Akt/mTOR C21H27N5O3 PFI-4 Epigenetic Reader Epigenetics C21H24N4O3 Domain BIO-acetoxime GSK-3 PI3K/Akt/mTOR C18H12BrN3O3 GSK2292767 PI3K PI3K/Akt/mTOR C24H28N6O5S SIS3 HCl TGF-beta/Smad TGF-beta/Smad C28H28ClN3O3 Larotrectinib (LOXO-101) Trk receptor Protein Tyrosine C21H24F2N6O6S sulfate Kinase PLX7904 Raf MAPK C24H22F2N6O3S VPS34-IN1 PI3K PI3K/Akt/mTOR C21H24ClN7O A-196 Histone Epigenetics C18H16Cl2N4 Methyltransferase LDC4297 (LDC044297) CDK Cell Cycle C23H28N8O SMI-4a Pim JAK/STAT C11H6F3NO2S Empagliflozin (BI 10773) SGLT GPCR & G C23H27ClO7 Protein TCS 359 FLT3 Angiogenesis C18H20N2O4S NSC 23766 Rho Cell Cycle C24H38Cl3N7 GDC-0349 mTOR PI3K/Akt/mTOR C24H32N6O3 Cobimetinib (GDC-0973, MEK MAPK C21H21F3IN3O2 RG7420) GW2580 CSF-1R Protein Tyrosine C20H22N4O3 Kinase BMS-345541 IκB/IKK NF-κB C14H17N5 Dynasore Dynamin Cytoskeletal C18H14N2O4 Signaling Venetoclax (ABT-199, Bcl-2 Apoptosis C45H50ClN7O7S GDC-0199) ICI-118551 Hydrochloride Adrenergic Receptor GPCR & G C17H28ClNO2 Protein AMG 337 c-Met Protein Tyrosine C23H22FN7O3 Kinase PF-CBP1 HCl Epigenetic Reader Epigenetics C29H37ClN4O3 Domain CPI-637 Epigenetic Reader Epigenetics C22H22N6O Domain BI-78D3 JNK MAPK C13H9N5O5S2 SB366791 TRPV Transmembrane C16H14ClNO2 Transporters Thiomyristoyl Sirtuin DNA Damage C34H51N3O3S CCT245737 Chk Cell Cycle C16H16F3N7O GSK6853 Epigenetic Reader Epigenetics C22H27N5O3 Domain SHP099 dihydrochloride phosphatase Others C16H21Cl4N5 Selonsertib (GS-4997) ASK Apoptosis C24H24FN7O KYA1797K Wnt/bleta-catenin Stem Cells & C17H11KN2O6S2 Wnt IPI-549 PI3K PI3K/Akt/mTOR C30H24N8O2 SGC2085 Histone Epigenetics C19H24N2O2 Methyltransferase Irbinitinib (ARRY-380, HER2 Protein Tyrosine C26H24N8O2 ONT-380) Kinase NMS-P118 PARP DNA Damage C20H24F3N3O2 BAY-876 GLUT Metabolism C24H16F4N6O2 VPS34 inhibitor 1 PI3K PI3K/Akt/mTOR C21H25N7O (Compound 19, PIK-III analogue) UK-371804 HCl Serine Protease Proteases C₁₄H₁₇Cl₂N₅O₄S GSK′872 (GSK2399872A) Serine/threonin kinase Apoptosis C19H17N3O2S2 LLY-283 Histone Epigenetics C17H18N4O4 Methyltransferase GSK180736A (GSK180736) ROCK Cell Cycle C19H16FN5O2 PD-166866 (PD166866) FGFR Angiogenesis C20H24N6O3 BLU-554 (BLU554) FGFR Angiogenesis C24H24Cl2N4O4 LY3214996 ERK MAPK C22H27N7O2S PF-06651600 JAK JAK/STAT C15H19N5O FM-381 JAK JAK/STAT C24H24N6O2 AZ31 ATM/ATR DNA Damage C24H28N4O3 Tofogliflozin(CSG 452) SGLT GPCR & G C22H28O7 Protein Omarigliptin (MK-3102) DPP-4 Proteases C17H20F2N4O3S Serabelisib (INK-1117, PI3K PI3K/Akt/mTOR C19H17N5O3 MLN-1117, TAK-117) FX1 Bcl-6 Apoptosis C14H9ClN2O4S2 Pamiparib (BGB-290) PARP DNA Damage C16H15FN4O NCT-503 Dehydrogenase Metabolism C20H23F3N4S Chk2 Inhibitor II (BML-277) Chk Cell Cycle C20H14ClN3O2 Ipragliflozin (ASP1941) SGLT GPCR & G C21H21FO5S Protein Nec-1s (7-Cl—O-Nec1) TNF-alpha Apoptosis C13H12ClN3O2 GSK′963 NF-κB, TNF-alpha NF-κB C14H18N2O GNF-6231 Wnt/beta-catenin Stem Cells & C24H25FN6O2 Wnt Skp2 inhibitor C1 (SKPin CDK Cell Cycle C₁₈H₁₃BrN₂O₄S₂ C1) PF-06840003 IDO Metabolism C12H9FN2O2 GI254023X Immunology & Immunology & C21H33N3O4 Inflammation related Inflammation BAY 1895344 (BAY- ATM/ATR DNA Damage C20H22ClN7O 1895344) Tenalisib (RP6530) PI3K PI3K/Akt/mTOR C23H18FN5O2 H3B-6527 FGFR Protein Tyrosine C29H34Cl2N8O4 Kinase Cu-CPT22 TLR Immunology & C19H22O7 Inflammation AZD1390 ATM/ATR PI3K/Akt/mTOR C27H32FN5O2 Atuveciclib (BAY-1143572) CDK Cell Cycle C18H18FN5O2S LXH254 Raf MAPK C25H25F3N4O4 WM-1119 Histone Acetyltransf Epigenetics C18H13F2N3O3S Evobrutinib BTK Protein Tyrosine C25H27N5O2 Kinase LIT-927 CXCR Immunology & C17H13ClN2O3 Inflammation 4-Hydroxyquinazoline Others antiplatelet C8H6N2O Valbenazine tosylate VMAT2 Others C38H54N2O10S2 SAR125844 c-Met Protein Tyrosine C25H23FN8O2S2 Kinase dBET1 Epigenetic Reader Do Epigenetics C38H37ClN8O7S GSK′547 TNF-alpha Apoptosis C20H18F2N6O Palbociclib (PD-0332991) CDK Cell Cycle C24H30ClN7O2 HCl Palbociclib (PD0332991) CDK Cell Cycle C26H35N7O6S Isethionate LDN-193189 2HCl TGF-beta/Smad TGF-beta/Smad C25H23ClN6 MCC950(CP-456773) Immunology & Immunology & C20H23N2NaO5S Inflammation related Inflammation bpV (HOpic) PTEN Others C6H4K2NO8V Erlotinib HCl (OSI-744) Autophagy, EGFR Protein Tyrosine C22H24ClN3O4 Kinase SGX-523 c-Met Protein Tyrosine C18H13N7S Kinase (−)-Huperzine A (HupA) GluR, AChR Neuronal C15H18N2O Signaling GSK256066 PDE Metabolism C27H26N4O5S CCT137690 Aurora Kinase Cell Cycle C26H31BrN8O Capmatinib (INCB28060) c-Met Protein Tyrosine C23H17FN6O Kinase EPZ005687 Histone Epigenetics C32H37N5O3 Methyltransferase GSK126 Histone Epigenetics C31H38N6O2 Methyltransferase Tazemetostat (EPZ-6438) Histone Epigenetics C34H44N4O4 Methyltransferase ISRIB (trans-isomer) PERK Apoptosis C22H24Cl2N2O4 A-1210477 Bcl-2 Apoptosis C46H55N7O7S Otenabant (CP-945598) HCl Cannabinoid Receptor GPCR & G C25H26Cl3N7O Protein FGF401 FGFR Protein Tyrosine C₂₅H₃₀N₈O₄ Kinase Lazertinib (YH25448, EGFR Protein Tyrosine C₃₀H₃₄N₈O₃ GNS-1480) Kinase

In some embodiments, different concentrations of the therapeutic agent are applied to the TOs in each partition or a group of replicate partitions. In certain embodiments, different therapeutic agents or combination of therapeutic agents are applied to the TOs in each partition or a group of replicate partitions. In certain embodiments, tumor organoids derived from different subjects are assessed.

Concurrently with or following the application of the therapeutic agent(s) to the TOs in the partitions, the TOs are contacted with one or more detection agents to assess for changes in morphological features or cell viability of individual cells in the TOs. In exemplary embodiments, the detection agents include fluorescent markers that can be visualized by fluorescent confocal imaging analysis. In particular embodiments, the markers include two or more markers for dead/apoptotic cells. Markers and assays useful for assessing dead apoptotic cells include, but are not limited to, IncuCyte® Caspase-3/7 Green Apoptosis Assay Reagent (Essen Biosciences cat #4440), and TO-PRO™-3 Iodide (642/661) (Fisher Scientific cat #T3605) and Annexin V assay (Abcam, ab14085).

In some embodiments, an additional detection agent is used to identify total cells in the tumor organoid sample. In some examples, all cells per organoid are measured by Hoechst 33342 staining, apoptotic cells per organoid are measured by Caspase 3/7 staining and dead/dying cells may are by TO-PRO-3 staining. Utilizing fluorescent markers for all cells and two markers for dead/apoptotic cells permits analysis of TOs at the single cell level and also permits generation of an absolute number of live and dead cells per organoid. This TO by TO analysis provides more information than simply calculating a relative value of viable cells from an entire well. Maintaining TO heterogeneity allows for determination of whether all cells are dying at a constant rate or if there is a mix of susceptible and resistant cells to a given treatment based on the distribution of viable cells per organoid. The aspects, such as the number of partitions (e.g., wells), types of plates, and types of cultures disclosed here, are exemplary in nature. Other aspects known in the art may be used instead or in combination with those aspects disclosed herein.

Following contact with the detection agents, the TOs are imaged and a tumor organoid profile is obtained from each image. In particular embodiments, the tumor organoid profile includes the number of TOs per image, the total number of cells (live and dead) present in each TO, the number of dead and dying cells present, and/or a cell viability value indicating the percentage of viable cells/tumor organoid. In some embodiments, the TOs are imaged on an inverted confocal microscope using the light microscopy and multiple fluorescent channels with varying wave-length excitation sources (e.g. laser or LED) and emission filters. In exemplary embodiments, an analysis module in a computer system is used to derive the tumor organoid profile from the images.

In some embodiments, tumor organoid profiles are acquired from at least 5, 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, 1×103, 1×104, or 1×105 tumor organoids per condition (e.g., a particular therapeutic dosage). In certain embodiments, the tumor organoid profiles are acquired at different time points. In some embodiments, the tumor organoid profiles acquired are used to generate a dose-response curve (see, e.g., Example 2 and FIG. 2 , below). In particular embodiments, a particular therapeutic dosage is assigned to a patient based on the dose-response curve. Also provided herein are methods for treating a patient having a cancer with a therapeutic agent based on a dosage derived using the subject method provided herein.

The high number of measurements recorded per condition (e.g., dose) allows the use of more complex statistical methods that would otherwise be unable to be used with a low-throughput dose response assay. In some embodiments, the tumor organoid profiles obtained are adjusted for one or more confounding technical effect. Use of a linear model allows for inclusion of covariates to adjust for potential confounding technical effects including initial TO viability, differences in growth rates between TOs derived from different patients, and different cancer types, and leverages all of the TO data to gain better statistical power. In some embodiments, a linear model is applied to determine differences between patients, or between drugs, at equivalent therapeutic concentrations (or doses).

In some embodiments, a brightfield image of the TO sample is obtained for each sample in addition to the cell death/viability data. In particular embodiments, tumor organoid profiles that include cell viability data (e.g., the percentage of viable cells in TO) and corresponding brightfield images for each TO sample at particular conditions (e.g., drug dosage conditions) are inputted into a classified trainer. In particular embodiments, the trainer is used to predict morphological changes (e.g., cell death or apoptosis) in a tumor organoid sample in response to a particular condition (e.g., dose of a therapeutic agent) based on a brightfield image of the sample (see Example 2 and FIG. 3 ).

In another aspect, provided herein are computer systems for carrying out the subject methods for assessing assess the effects of an agent (e.g., a therapeutic agent) on tumor organoids (TOs). In some embodiments, the computer system includes at least one processor and a memory storing at least one program for execution by the at least one processor, the at least one program includes instructions for carrying out one or more steps of the subject methods.

In some embodiments, the disclosure provides methods and systems for evaluating an effect of a cancer therapeutic agent. In some embodiments, the method includes providing a plurality of tumor organoids cultured in a tumor organoid culture medium, where the plurality of tumor organoids is divided into a plurality of tumor organoid subsets. The method then includes contacting each subset in the plurality of tumor organoid subsets with a cancer therapeutic agent. The method also includes contacting each subset in the plurality of tumor organoid subsets with one or more cell death detection agents and a total cell detection agent. The method then includes obtaining a tumor organoid profile for each subset in the plurality of subset. In some embodiments, the tumor organoid profile includes a cell viability value for every tumor organoid in the subset. The method then includes assessing the effect of the cancer therapeutic agent based on the tumor organoid profiles.

In some embodiments, the disclosure provides methods and systems for assigning a treatment dosage of a cancer therapeutic agent for a subject in need thereof. In some embodiments, the method includes providing a plurality of tumor organoids cultured in a tumor organoid culture medium, where the tumor organoids are derived from a subject, and where the plurality of tumor organoids is divided into a plurality of tumor organoid subsets. The method then includes contacting each subset in the plurality of tumor organoid subsets with a different dosage of a cancer therapeutic agent. The method also includes contacting each subset in the plurality of tumor organoid subsets with one or more cell death detection agents and a total cell detection agent. The method then includes obtaining a tumor organoid profile for each subset in the plurality of subset, where the tumor organoid profile includes a cell viability value for every tumor organoid in the subset. The method then includes determining a therapeutic agent dosage curve from the tumor organoid profiles. The method then includes assigning a treatment dosage of the cancer therapeutic agent to the subject based on the therapeutic agent dosage curve.

EXAMPLES Example 1 PARPi Sensitivity of BRCA1⁻/BRCA2⁻ Tumors

Tumor biopsies were collected from four individuals: UK1393, 10423-12001, 10524-12001, and 10941-12002. The tumors were genotyped and determined not carry BRCA1 or BRCA2 mutations. As such, according to conventional guidance, the tumors are not indicated for first-line therapy with a PARP inhibitor. In order to test whether these tumors may still be sensitive to PARP inhibitors, despite not carrying a BRCA1 or BRCA2 mutation, tumor organoids were cultured using cells from the biopsied material.

Briefly, cells within each of the biopsied tumor samples were dissociated and cultured to establish a tumor organoid culture line from the tumor of each individual. Single tumor organoids from the tumor organoid culture lines were collected and plated, individually, into wells of a multiwell plate with culture medium. A series of six concentrations of olaparib, in a 5-fold serial dilution, were established for the tumor organoids derived from each individual, as well as negative controls. After incubation with olaparib, a caspase 3/7 apoptosis assay was performed in each well, to determine the sensitivity of each tumor organoid to the respective concentration of olaparib. Results of the caspase dilution series experiments are plotted in FIG. 3 .

As expected, since the tumors did not carry a BRCA1 or BRCA2 mutation, three of the tumor organoid culture lines were fairly insensitive to olaparib: 10423-12001 (FIG. 3B), 10524-12001 (FIG. 3C), and 10941-12002 (FIG. 3D). However, unexpectedly, tumor organoid culture line UK1393 was more than 100-fold more sensitive to olaparib, despite being derived from a tumor that did not carry a BRCA1 or BRCA2 mutation. These results suggest that the cancer in this individual may be effectively treated with a PARP inhibitor as a first-line therapy, despite not carrying a biomarker conventionally associated with PARP inhibitor efficacy.

Example 2 Drug Screening Platform

Patient derived Tumor Organoids (TOs) are emerging as patient-representative models that recapitulate clinical responses to candidate therapeutics. Yet standard methods of interpreting in vitro treatments of TOs have been developed from monoclonal, rapidly proliferating 2D cell lines that are not amenable for TOs which have limited biomass and intra-tumoral clonal heterogeneity. To address these challenges, a drug screening platform more applicable for the unique characteristics of TOs was developed and optimized. The platform couples high content fluorescent confocal imaging analysis with a robust statistical analytical approach to measure hundreds of discrete data points of TO viability from as few as 10{circumflex over ( )}3 cells. This approach was validated through evaluating responses to hundreds of small molecule inhibitors as well as a panel of chemotherapeutic agents in TO models derived from different patients.

The platform was highly reproducible with minimal intra- and inter-assay variance (well:well variance=ns, plate:plate variance=ns, by ANOVA). QC of TOs was performed to remove outlier TOs by size and remaining TOs were normalized by mean vehicle proportion survival. To compare differential therapeutic toxicity between TOs from different patients, a linear model was developed to evaluate differences in proportion of surviving cells across equivalent therapeutic concentrations, identifying highly significant differences (P<10⁻¹²). Intriguingly, the linear model not only uncovered heterogeneity of responses between TOs derived from different patients, but also identified organoid clonal populations derived from the same patient with differential drug response offering a window into uncovering functional intratumoral heterogeneity.

Lastly, throughput was substantially increased by applying a machine learning algorithm to predict therapeutic response via TO morphological changes from light microscopy. Employing this algorithm eliminated the need for fluorescent labeling leading to increased assay throughput by 3-4 fold amounting to 96 and 384 well plate acquisitions in as little as 5 and 15 minutes respectively. As such provided herein is a high-throughput capable of measuring TO therapeutic response with high statistical confidence and exquisite inter-assay reproducibility. This approach can be utilized in research settings to elucidate heterogeneity of therapeutic responses within and among patients, and may be utilized in the clinical laboratory to potentially guide precision oncology treatments.

Cell Plating

A drug screening platform may be utilized to assess the effectiveness of drugs or other agents on tumor organoids (TOs). Single cell suspensions of tumor organoid cells are generated as described below.

-   -   1. Gently remove the medium from the tumor organoids (TOs) by         pipetting out the medium. Do not use vacuum to aspirate the         medium.     -   2. Add 500 mL of TrypLE Express to each well, attempting to         disrupt the organoid containing Matrigel domes.     -   3. Scrape the remaining Matrigel off the bottom of the wells         with 1 mL pipette.     -   4. Place the dissociated organoids into a 15 ml low-binding         centrifuge tube.     -   5. Place the tube in the 37° C. water bath for 15 min.     -   6. Spin the cells at 200 g for 5 min. in a 4° C. centrifuge.     -   7. Carefully pipet out and discard the supernatant.     -   8. Add 1 ml of DPBS to the cell pellet.     -   9. Centrifuge the cell containing tube at 4° C. at 200 g for 5         min.     -   10. Pipet out the supernatant and add any medium/reagent         required for your following procedure.

In one example, TOs from 24-well plate culture are dissociated to single cells and seeded in 384-well plates in a mix of 30% Matrigel and 70% media. This allows TOs to form from individual cells for the assay, maintaining TO heterogeneity in each well. The cells are seeded at 2,000 cells per well allowing a sufficient number of TOs to form while not overcrowding the plate so that TOs do not overlap or touch allowing for easy identification of individual TOs.

Drug and Detection Reagent Application

Caspase 3/7 Green Apoptosis Assay Reagent (Essen Biosciences cat #4440) is diluted in media to 2.5 μM. Drugs are diluted to 20 μM in media with Caspase 3/7 reagent and 10-fold serial dilutions are prepared in a separate 384-well plate. Diluted drugs are added to the 384-well assay plate by pipetting 20 μl of the diluted drug, media, Caspase 3/7 mix to the appropriate wells using an Integra Viaflo automated pipetting system.

In one example, one or more chemotherapeutic agents may be applied to the TOs in the well plates. Example agents include Paclitaxel, Gemcitabine, Cisplatin, Carboplatin, Oxaliplatin, Capecitabine, SN-38 (CPT-11), 5-FU, MTX (methotrexate), Docetaxel, Bortezomib, Everolimus, Ulixertinib, Dasatinib, Vinblastine, Nelarabine, Epirubicin, Afatinib, Lapatinib, Cytarabine, Cladribine, Doxorubicin, Azacitidine, and Staurosporine. Other examples include classes of drugs including but not limited to: taxanes, platinating agents, vinca alkaloids, alkylating agents, and anthracyclines.

Example 3 High Content Fluorescent Confocal Imaging Analysis

TOs may be stained using common vital dyes to measure cellular behaviors amenable for high content fluorescent confocal imaging analysis. In one example, TOs are stained with Hoechst 33342 (Fisher Scientific cat #H3570), IncuCyte® Caspase-3/7 Green Apoptosis Assay Reagent (Essen Biosciences cat #4440), and TO-PROTM-3 Iodide (642/661) (Fisher Scientific cat #T3605) in multi-well tissue culture plates (e.g. 24, 48, 96, 384, etc.). After staining, TOs are imaged on an inverted confocal microscope using the light microscopy and multiple fluorescent channels with varying wave-length excitation sources (e.g. laser or LED) and emission filters. Each channel (i.e. light microscopy, Hoechst nuclear stain, FITC, Cy5) is acquired through an objective lens, in one example a 10× objective lens is used to take images at two sites per well with a stack of images in the Z plane ranging from 1-100 heights in the Z-plane with increments ranging from submicron to as high as 15 micron per Z-plane height. Z-stack images are projected to 2D and analyzed using image analysis software with parameters to identify TOs based on the pixel intensities in the nuclear stain channel (i.e. Hoechst 33342 channel) and the size of the object by measurements in 2D space of the object as well as number of nuclei. All cell nuclei are identified by Hoechst 33342 staining. TOs are identified by clusters of nuclei identified by Hoechst 33342 staining. Apoptotic cells are identified by Caspase 3/7 staining and dead cells are identified by TO-PRO-3 staining overlapping with Hoechst 33342 staining. The analysis module is used to enumerate TOs per image, how many cells (live and dead) are present in each TO, and how many dead and dying cells are present in each TO by Caspase 3/7 and TO-PRO-3 staining separately. The Caspase 3/7 and TO-PRO-3 stains provide two independent counts of dead and dying cells.

Utilizing fluorescent markers for all cells and two markers for dead/apoptotic cells permits analysis of TOs at the single cell level and also permits generation of an absolute number of live and dead cells per organoid. This TO by TO analysis provides more information than simply calculating a relative value of viable cells from an entire well. Maintaining TO heterogeneity allows for determination of whether all cells are dying at a constant rate or if there is a mix of susceptible and resistant cells to a given treatment based on the distribution of viable cells per organoid. The aspects, such as the number of wells, types of plates, and types of cultures disclosed here, are exemplary in nature. Other aspects known in the art may be used instead or in combination with those aspects disclosed herein.

FIG. 4 shows an example image of high-content fluorescent confocal imaging analysis. (A-D) Brightfield (gray scale), Hoechst 33342 (blue), Caspase 3/7 (green), and TO-PRO-3 (red) staining is shown for vehicle control (A and B) and staurosporine treated (C and D) gastric cancer tumor organoids. (B and D) Overlays of the fluorescent channels and the result of image analysis are shown side by side. Light-blue coloring on the image analysis indicates the area of a given tumor organoid. Live (purple) and dead (red) cells are shown in the image analysis panels. Scale bars represent 100 microns.

Example 4 Statistical Approach

Since data are collected from hundreds of TOs per drug condition, hundreds of data points may be analyzed within an experimental replicate usually a single culture well in a multiwell plate, rather than just collecting one data point from each experimental replicate well as is typically done in drug screens. The percent viable cells (which may be determined by a lack of Caspase 3/7 and/or TO-PRO-3 staining) is calculated for each individual TO. The percent viable cells per organoid from each technical replicate is then averaged together for the actual percent viable cells per drug concentration. These values are normalized to the percent viable cells per TO of the DMSO treated vehicle control and plotted to generate a dose-response curve.

Table 3 contains a small example of the data output. Each row of the table represents an individual organoid. The columns contain information for which well of the culture plate was imaged (Well Name), the size of the TO (TO area), the total number of cells in the organoid (All cells (TO-PRO-3) and All cells (Caspase 3/7)), the number of dead cells by positive TO-PRO-3 staining (Dead cells (TO-PRO-3)), the number of live cells by negative TO-PRO-3 staining (Live cells (TO-PRO-3)), the number of dead cells by positive Caspase 3/7 staining (Dead cells (Caspase 3/7)), and the number of live cells by negative Caspase 3/7 staining (Live cells (Caspase 3/7)).

TABLE 3 Well All cells Live cells Dead cells All cells Live cells Dead cells Name TO Area (TO-PRO-3) (TO-PRO-3) (TO-PRO-3) (Caspase 3/7) (Caspase 3/7) (Caspase 3/7) O02 410.178223 2 1 1 2 2 0 O02 152.455612 1 0 1 1 0 1 O02 319.430817 1 0 1 1 0 1 O02 3570.00244 0 0 0 0 0 0 O02 212.348892 1 0 1 1 0 1 O02 246.832901 1 0 1 1 0 1 O02 348.469971 1 0 1 1 0 1 O02 2268.68481 7 0 7 7 0 7 O02 132.491196 1 0 1 1 0 1 O02 1969.21838 7 1 6 7 0 7 O02 1069.00427 4 1 3 4 1 3 O02 373.879242 1 0 1 1 0 1 O02 176.049942 1 0 1 1 0 1 O02 1386.62012 4 0 4 4 0 4 O02 214.163849 1 0 1 1 0 1 O02 397.473572 1 0 1 1 0 1 O02 343.025146 1 0 1 1 0 1 O02 346.655029 1 0 1 1 0 1 O02 840.320862 2 1 1 2 1 1 O02 208.718994 1 0 1 1 0 1 O02 264.982391 1 0 1 1 0 1 O02 464.626648 1 0 1 1 0 1 O02 947.402771 2 0 2 4 0 4 O02 446.477173 1 0 1 1 0 1 O02 568.078674 3 0 3 3 0 3 O02 431.957581 2 0 2 2 0 2 O02 713.274475 2 0 2 2 0 2 O02 110.711815 1 0 1 1 0 1 O02 980.071838 3 1 2 3 0 3

FIG. 5 shows an example dose-response curve for cell viability by TO-PRO-3 (left) and Caspase 3/7 (right) after treatment with staurosporine on tumor organoids derived from a gastric cancer. Each point represents the mean±SD from 450-1200 individual organoids.

Hundreds of discrete measurements of TO viability per drug concentration can be made, beginning with as few as 6x10⁵ cells. These measurements may be performed for every cell of every organoid. There are hundreds of organoids per experimental condition such as incubation with a drug at a specific concentration with approximately between 3-15 cells per organoid.

Additionally, high reproducibility with minimal inter- and intra-assay variance can be achieved using the subject platform.

Due to the large number of TOs being measured per well, there is a high number of sampling occurring to identify the true mean. Just as one arrives at a high precision of 0.1666666 probability of rolling a six on a standard die if one rolls the die 600 times instead of just 6 times. The high accuracy of finding the true mean means that interwell reproducibility is high and inter assay reproducibility is also high.

To compare differential therapeutic toxicity between TOs from different patients, a linear model was developed to evaluate survival across equivalent therapeutic concentrations.

The high number of measurements recorded per dose allows the use of more complex statistical or non-statistical methods that would otherwise be unable to be used with a low-throughput dose response assay. Therefore, a linear model was used (Galton, 1886, “Regression Towards Mediocrity in Hereditary Stature,” The Journal of the Anthropological Institute of Great Britain and Ireland 15: 246-263) to determine differences between patients, or between drugs, at equivalent therapeutic concentrations (or doses). Use of a linear model allows for inclusion of covariates to adjust for potential confounding technical effects including initial TO viability, differences in growth rates between TOs derived from different patients, and different cancer types, and leverages all of the TO data to gain better statistical power.

For example, to determine differences in viability to a 10 uM dose of staurosporine compared to a 10 uM dose of Olaparib that were run on different experiments (plates), we would run the following model and estimate the betas and corresponding p-values for each main effect (x_(drug), and x_(plate)). Since we estimate both the drug and plate effect, we can control for potential experimental noise generated by the experiment being run on different plates.

Y_(normalized viability proportion)˜βx_(drug)+βx_(plate)+ε

In a different example, differences in viability to a 1 nM dose of Dapagliflozin between TO cell lines that were run by different technicians is determined. Here, differences between TO lines (estimating the beta for x_(cell line)) and determined, with control for experimental noise that might be due to different technicians running the assay:

Y_(normalized viability proportion)˜βx_(cell line)+βx_(technician)+ε

Lastly, throughput was substantially increased by applying a deep learning algorithm to the high-dimensional dataset. The algorithm was adapted from the Generative Adversarial Network Pix2pix by Phillip Isola et al, 2018, “Image-to-Image Translation with Conditional Adversarial Networks,” arXiv:1611.07004v3 [cs.CV] 26Nove2018, which is hereby incorporated by reference. The GAN architecture makes use of a generator model that is trained to generate meaningful data (typically from noise), and a discriminator model that is trained to distinguish between what's real and what's been generated.

Pix2pix is a specific type of GAN designed for general purpose Image-to-Image translation involving the controlled conversion of a source image to target image. Here, pix2pix was employed to transfer the style of brightfield images to fluorescent images.

FIG. 6 shows two examples of predictions on a test set where the brightfield image is shown in the far left column, the model generated fluorescent image is shown in the middle column, and is the actual fluorescent image is shown in the far right column. As shown in FIG. 6 , the trained model accurately predicted morphological responses to pharmacological agents based on brightfield images, thus potentially reducing a 384 well plate reading to as little as several minutes.

In summary, the systems and methods described here may measure therapeutic response in patient derived tumor organoids with high statistical confidence and technical reproducibility. The approach may be utilized in both research and clinical settings to better understand heterogeneity of therapeutic responses within and among patients, and further guide precision oncologic decision-making.

Example 5 Example PARP inhibitor Drug Screen

A recent development in precision oncology is the use of poly (ADP-ribose) polymerase (PARP) inhibitors in patients whose tumors exhibit evidence of homologous recombination deficiency (HRD), especially in cases of somatic loss of BRCA1 or BRCA2, or LOH of functional BRCA1/2 alleles in patients with inherited non-functional BRCA1/2 alleles.

To advance TO utility for drug development and precision medicine, a universal label-free TO drug screening assay was developed. Without sacrificing throughput, this neural network prediction of drug response from light microscopy achieved high reproducibility compared to previously described metabolic-based assays (Tiriac et al., Cancer Discov 8, 1112-1129 (2018); Tiriac et al., Isolation and Characterization of Patient-derived Pancreatic Ductal Adenocarcinoma Organoid Models. J Vis Exp. (2020); Vlachogiannis et al., Science 359, 920-926 (2018)). Importantly, the network identified clinically relevant drug responses across a broad range of cancer-types including PARPi response from HRD-positive and -negative TOs. Notably, the PARPi responses in this small cohort of organoids were generally higher in HRD-positive TOs, with certain drugs exhibiting more potency in vitro than others. These observations confirm previous studies in patients (Coleman et al., Lancet 390, 1949-1961 (2017)) and short-term ovarian cancer organoid cultures (Hill et al., Cancer Discov 8, 1404-1421 (2018)). In addition, the RCA network identified response to afatinib associated with a high ERBB2 (HER2) amplification in the gastric TO. The distribution of response among the TO populations was demonstrative of functional intratumoral heterogeneity, as evidenced by a subset of the organoid population exhibiting resistance to afatinib. When correlated with the patient's clinical course, we found that the biopsy used to establish this TO line was obtained during disease progression on anti-ERBB2 therapy. Identifying heterogeneity in drug response has the potential to uncover mechanisms of primary resistance to novel therapeutics and may also provide predictive and prognostic information for treatment response in personalized clinical assays

To provide proof-of-concept for this precision medicine approach, we evaluated ten TO lines (breast, endometrial, colon, ovarian, and NSCLC) based on HRD status. We assessed genome-wide LOH and categorized TOs as either HRD-positive or HRD-negative (Timms et al., Breast Cancer Research 16, 475 (2014); Yi et al., International Journal of Cancer 145, 1209-1220 (2019)). We then exposed TOs to a panel of FDA-approved PARP inhibitors and compared predicted drug responses, based on a trained neural network, to fluorescent-based readouts. We found the network predictions were strongly correlated with fluorescent-based drug responses across all cancer types (FIG. 7 ). Additionally, the classifier's measurement of PARPi response was able to discriminate between HRD-positive and HRD-negative organoids, comparable to fluorescent-based measurements (FIG. 8 ). Thus, the network-based assay accurately predicts clinically relevant drug responses.

Methodology

Tumor specimens were received from multiple institutions and processed for organoid culture at a CLIA-certified, CAP-accredited laboratory. All specimens were collected from consented patients under protocols monitored by the Institutional Review Board at each institution. The specimens were placed into iced RPMI (Lifetech) and processed the same day or after overnight storage at 4° C. The specimens were then digested to single-cell suspension with a GentleMACs instrument using the Miltenyi Tumor Dissociation kit (Miltenyi Biotec) according to the manufacturer's protocol.

Development and Culture of Tumor Organoids

Tumor organoids (TOs) were developed using an adapted epithelial cell-only submerged Matrigel culture technique (Sato et al., Nature 459, 262-265 (2009)). Briefly, cells were seeded at a density of 400 cells/μl in a 50 μl droplet of GFR Matrigel matrix (Corning) and grown in 24-well, flat-bottom tissue culture plates (Eppendorf). Growth medium was changed twice weekly and TOs were passaged every 1-2 weeks as needed. For passaging, growth media was removed, and Matrigel domes were disrupted mechanically by adding 500 μl TrypLE Express Enzyme (GIBCO) per well. TOs were transferred to 15-ml conical tubes and incubated in a 37° C. water bath for 10 minutes. Cells were then centrifuged at 200×g for 3 minutes and resuspended in 2 ml DPBS. Cells were resuspended in GFR Matrigel Matrix at 400 cells per microliter, and 50 μl domes were plated in pre-warmed, 24-well, flat-bottom plates and left to polymerize in a 37° C. incubator before the addition of 500 μl growth medium and 10 μM Y-27632 (Bio-techne) per well.

TO cultures were maintained in serum-free defined media conditions based on the consensus of previous reports for anticipated tumor types; namely, Advanced DMEM/F12 nutrient mix supplemented with B27, nicotinamide, n-acetylcysteine, recombinant growth factors EGF, Noggin, R-spondinl (RSPO-1), Wnt-3A, FGF-2, 7, and 10, and small molecule inhibitors of p38 MAPK and TGF-beta.

Tumor Organoid Growth Analysis

Two independent observers determined organoid formation and serial passaging. Cells that demonstrated exponential increase in biomass on serial passage were deemed high proliferation and were cryopreserved in Recovery Cell Culture Freezing media (Gibco) when biomass reached >10⁶ cells, following the manufacturer's protocol.

For quantitative organoid growth measurements, bright-field images of 24-well plates containing TOs were captured at a minimum of two different time points for the same passage using the ImageXpress Micro Confocal high-content imaging system (Molecular Devices, Calif.). The average total area sum of TOs was then plotted by time and the maximum growth rate was calculated by linear regression.

Pathologic Evaluation

Cultures were intermittently selected for formalin fixation and were prepared for H&E staining either via paraffin embedding or cyto-spin. H&E stains of organoid cultures from 320 patients were interpreted by a board-certified pathologist (GK) using histologic and cytologic features. Due to the use of growth factors, cultures displayed features of cellular proliferation including nuclear hyperchromasia with slight pleomorphism, increase in nuclear to cytoplasmic ratio and conspicuous nucleoli. Mitotic figures were frequent with few atypical forms. As such, the identification of malignant cells on the basis of cytologic features was obscured and was therefore based on the degree of these changes and the presence of marked loss of polarity and macronucleoli.

Sample Processing and Nucleic Acid Isolation

Organoids were dissociated using TrypLE Express Enzyme (GIBCO) and dissociated cells were immediately lysed in 350 μL of buffer RLT from the Allprep DNA/RNA Micro Kit (Qiagen) and stored at −80° C. Upon thawing, cell lysates were homogenized using QlAshredder spin columns (Qiagen). DNA and RNA were isolated using the Allprep DNA/RNA Micro Kit per manufacturer's instructions.

HLA-typed PBMC controls used for flow cytometry analysis were commercially procured as cryovials. PBMCs were thawed, washed, and resuspended in RPMI growth medium containing 10% FBS and 2 mM L-glutamine. Cells were left to recover for 1 hr at 37° C.

Next-Generation Sequencing

Next-generation sequencing was conducted as previously described (Beaubier et al., 2019a; Beaubier et al., 2019b). Briefly, nucleic acids were library prepped using a targeted gene panel as previously described, loaded on an Illumina HiSeq 4000 (Illumina), and DNA tumor libraries were sequenced to an average unique on-target depth of 500×. Similarly, RNA was prepared using an exome-capture RNA-Seq protocol and sequenced on the Illumina HiSeq 4000 platform. Variant calls and other molecular signatures, such as copy-number alterations, fusion events, and mRNA gene expression levels, were called and reported based on established guidelines.

Associations of Clinical and Molecular Features with Sustainable Growth

Clinical features including tissue site, T stage, N stage, M stage, race (caucasian, Asian, African-american, other), sex, neoadjuvant therapy treatment, and biospecimen features such as cell count and cold ischemia time (>12 hours) were structured as binary values and evaluated as a generalized linear model. Logistic regression was then applied to model high-proliferation organoid growth as a linear combination of clinical features using the stats R package (v3.5.2).

Analysis of single-nucleotide variants (SNV), copy-number alterations (CNA), and transcriptome profiling was performed using a NGS assay (Beaubier et al., Nat Biotechnol 37, 1351-1360 (2019); Beaubier et al., Oncotarget 10, 2384-2396 (2019)). The combined effect of pathogenic variants within a gene classified by the assay platform were then tested using a gene-based test as implemented in SKAT-o (Lee et al., American journal of human genetics 91, 224-237 (2012)). Gene-based tests were performed within each cancer and combined across cancers. Transcriptome analysis was performed as described below.

Copy-number calls were determined for paired probes by an internal algorithm that considered tumor purity and sequencing depth in a two-pass approach. First, segmentation of chromosomal regions was performed to define chromosomal regions with specific copy numbers using panel coverage data and transformed to provide probe-level copy-number values. Next, the segment data was used in a second algorithm to approximate integer copy-number values for major (total observed copies at a given loci) and minor allele count as well as estimates for tumor purity, ploidy, and B-allele frequencies (BAF). Following segmentation, copy number and tumor purity were assessed using a grid search methodology. Starting from the initial estimate of the tumor purity lower bound, a copy-number state matrix was generated containing total/minor copy state combinations and their expected log ratios and logBAF given the initialized tumor purity. Each segment was projected into the matrix and the log probability that it belonged to each analyzed copy state was computed based on drawing from a normal probability density function defined by the expected log-ratio and the pre-computed log ratio standard deviation. The same process was applied for logBAF with a sliding-weight scale based on the number of heterozygous germline variants observed within the segment. This was done to account for noise in logBAF in the context of sparse observations.

Drug Screen and Image Analysis

A 320-drug panel was purchased from Selleckchem, which is detailed on their website (found online at selleckchem.com/screening/selective-library.html). Additional compounds are included in STAR methods.

TOs were dissociated as described above and resuspended in a 30:70% mix of GFR Matrigel:growth media at a concentration of 100 cells/μl. The solution was added to 384-well assay plates (Corning) at 20 μl per well for a final concentration of 2,000 cells per well. Assay plates were covered with a Breathe-Easy sealing membrane (Sigma Aldrich) to prevent evaporation. TOs were grown for 72 hours before drug addition. Drugs were prepared in growth media with 2.5 μM Caspase-3/7 Green Apoptosis Assay Reagent (Essen Bioscience). Serial dilutions of each molecule were prepared in 384-well polystyrene plates (Nunc). Diluted drug was added to the assay plate using an Integra Viaflo pipette (Integra) mounted on an Integra Assist Plus Pipetting Robot (Integra). Assay plates were again covered with a Breathe-Easy sealing membrane and TOs were exposed to drugs for another 72 hours before imaging.

Prior to imaging, TOs were incubated with 4 μM Hoechst 33342 (Fisher Scientific) and 300 nM TO-PRO-3 Iodide (642/661) (Invitrogen) for 1.5-2 hours. Assay plates were imaged using an ImageXpress Micro Confocal (Molecular Devices) at 10× magnification so that ˜100-200 TOs were imaged per well. Images were acquired as 4×15 μm Z-stacks and the 2D projections were analyzed to assess cell viability. Confocal images were analyzed using the MetaXpress software (Molecular Devices) custom module editor feature to design an analysis module that identified TOs by clusters of Hoechst 33342 staining, individual cells by Hoechst 33342 staining, and dead/dying cells by either TO-PRO-3 or Caspase-3/7 staining. The result of this analysis module is a spreadsheet detailing the number of live and dead cells for every individual organoid.

The percentage of viable cells per organoid was calculated based on the image analysis described above. Organoids with fewer than three cells and larger than the top one percent by size were excluded from analysis. The mean viability for all organoids at a given drug concentration was used in dose-response curves to calculate AUC. AUC was calculated using the computeAUC function using settings for “actual” AUC of the R Package PharmacoGx (v1.17.1). Heatmaps of AUC values were generated using the Pheatmap package (v1.0.12) in R. Scatterplots of AUC values were generated using the ggplot2 package (v3.3.0) in R.

Response and Label-Free Prediction from Brightfield Images

The multiplexed fluorescence images were 1024×1024×3 RGB images, where red corresponds to dead cells (TO-PRO-3), green to apoptotic cells (Caspase-3/7), and blue to nuclei (Hoechst 33342). All wavelength channels underwent a simple intensity rescaling contrast enhancement technique to brighten and sharpen the TOs/cells as well as remove background noise. The mean viability for all organoids per site was obtained from the MetaXpress software readout.

Example 6 PARPi Sensitivity in Colorectal Cancer Tumor Organoids

In this example, PARPi sensitivity was measured for two colorectal tumor organoids (TOs). Each TO or source tissue associated with the TO (for example, a patient biopsy used to generate the TO) were genetically sequenced to determine whether the TO had variants (mutations) in homologous recombination proteins (including BRCA1 and BRCA2) and whether the TO was likely to have homologous recombination deficiency (HRD), according to an HRD engine.

None of the TOs had pathogenic single nucleotide variants (SNVs) in BRCA1 or BRCA2. None of the TOs had loss of heterozygosity (LOH) of BRCA1 or BRCA2. None of the TOs had bi-allelic loss of BRCA1 or BRCA2 (both a pathogenic SNV and LOH) and traditionally would not have been expected to have HRD or respond to PARPi therapy. BRCA mutation and LOH status was based on sequencing analysis of either the TO or the source tissue.

Regardless of the lack of bi-allelic BRCA loss, some of the TOs were analyzed by an HRD engine and predicted to have HRD based on other criteria.

The HRD engine is described in U.S. patent application Ser. No. 16/789,363, titled “An Integrated Machine-Learning Framework To Predict Homologous Recombination Deficiency”, filed Feb. 12, 2020, the contents of which are incorporated by reference herein in their entirety for any and all purposes. In another embodiment, the HRD score or likelihood of PARPi sensitivity may be determined by the trained classifier disclosed herein.

One of the TOs had a low HRD score (unlikely to have HRD or be sensitive to PARPi) and one of the TOs had a high HRD score (likely to have HRD and be sensitive to PARPi).

All of the TOs were grown in culture wells and each well was exposed for 96 hours to either a negative control (1% DMSO) or one of multiple PARPi therapies (Rucaparib, Niraparib, Pamiparib, Talazoparib, Olaparib, or Veliparib) at one of three concentrations (1 nM, 100 nM, or 10,000 nM). Some of the organoids were exposed to additional concentrations as noted in the x-axis of the figures.

At 96 hours the cells were stained by either caspase 3/7 or TO-PRO-3 (caspase 3/7 stained dying, apoptic cells and TO-PRO-3 stained dead cells). For each PARPi therapy, efficacy was measured at each concentration by detecting the proportion of viable cells that were not stained and normalizing that proportion to the proportion of viable cells in the negative control well, where the proportion of negative control well cells that were viable was adjusted to 100% or 75% (indicated in the figure). This normalization resulted in some experimental wells having a proportion of viable cells that was greater than 100% (or 75%). A best fit curve was generated for the viability proportion at each concentration and an inverse AUC was calculated as the area between actual cell viability (the best fit curve) and 100% (or 75%) cell viability. The inverse AUC served as an additional measure of PARPi efficacy, where a higher inverse AUC indicated a higher drug efficacy.

The PARPi therapies were hypothesized to be more effective against TOs with a high HRD score than TOs with a low HRD score.

The viability data shown below indicate that the PARPi therapies were more effective against TOs with a high HRD score than TOs with a low HRD score.

For organoids that were PARPi sensitive, PARPi therapies were effective against TOs that did not have BRCA1 or BRCA2 mutations or biallelic inactivation of BRCA1 or BRCA2.

FIGS. 9A and 9B illustrate viability data for a tumor organoid having a low HRD score, a pathogenic BRCA1 mutation, no BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 10A and 10B illustrate viability data for a colorectal tumor organoid having a high HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

Example 7 PARPi Sensitivity in Breast Cancer Tumor Organoids

In this example, PARPi sensitivity was measured for three tumor organoids (TOs). Each TO or source tissue associated with the TO (for example, a patient biopsy used to generate the TO) were genetically sequenced to determine whether the TO had variants (mutations) in homologous recombination proteins (including BRCA1 and BRCA2) and whether the TO was likely to have homologous recombination deficiency (HRD), according to an HRD engine.

None of the TOs had pathogenic single nucleotide variants (SNVs) in BRCA1 or BRCA2. None of the TOs had loss of heterozygosity (LOH) of BRCA1 or BRCA2. None of the TOs had bi-allelic loss of BRCA1 or BRCA2 (both a pathogenic SNV and LOH) and traditionally would not have been expected to have HRD or respond to PARPi therapy. BRCA mutation and LOH status was based on sequencing analysis of either the TO or the source tissue.

Regardless of the lack of bi-allelic BRCA loss, some of the TOs were analyzed by an HRD engine and predicted to have HRD based on other criteria.

The HRD engine is described in U.S. patent application Ser. No. 16/789,363, titled “An Integrated Machine-Learning Framework To Predict Homologous Recombination Deficiency”, filed Feb. 12, 2020, the contents of which are incorporated by reference herein in their entirety for any and all purposes. In another embodiment, the HRD score or likelihood of PARPi sensitivity may be determined by the trained classifier disclosed herein.

Two of the TOs had a low HRD score (unlikely to have HRD or be sensitive to PARPi) and one of the TOs had a high HRD score (likely to have HRD and be sensitive to PARPi).

All of the TOs were grown in culture wells and each well was exposed for 96 hours to either a negative control (1% DMSO) or one of multiple PARPi therapies (Rucaparib, Niraparib, Pamiparib, Talazoparib, Olaparib, or Veliparib) at one of three concentrations (1 nM, 100 nM, or 10,000 nM). Some of the organoids were exposed to additional concentrations as noted in the x-axis of the figures.

At 96 hours the cells were stained by either caspase 3/7 or TO-PRO-3. Caspase 3/7 stained dying, apoptic cells and TO-PRO-3 stained dead cells. For each PARPi therapy, efficacy was measured at each concentration by detecting the proportion of viable cells that were not stained and normalizing that proportion to the proportion of viable cells in the negative control well, where the proportion of negative control well cells that were viable was adjusted to 100% or 75% (indicated in the figure). This normalization resulted in some experimental wells having a proportion of viable cells that was greater than 100% (or 75%). A best fit curve was generated for the viability proportion at each concentration and an inverse AUC was calculated as the area between actual cell viability (the best fit curve) and 100% (or 75%) cell viability. The inverse AUC served as an additional measure of PARPi efficacy, where a higher inverse AUC indicated a higher drug efficacy.

The PARPi therapies were hypothesized to be more effective against TOs with a high HRD score than TOs with a low HRD score.

The viability data shown below indicate that the PARPi therapies were more effective against TOs with a high HRD score than TOs with a low HRD score.

For organoids that were PARPi sensitive, PARPi therapies were effective against TOs that did not have BRCA1 or BRCA2 mutations or biallelic inactivation of BRCA1 or BRCA2.

FIGS. 11A and 11B illustrate viability data for a tumor organoid having a low HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 12A and 12B illustrate viability data for a tumor organoid having a low HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 13A and 13B illustrate viability data for a tumor organoid having a high HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

Example 8 PARPi Sensitivity in Ovarian Cancer Tumor Organoids

In this example, PARPi sensitivity was measured for two ovarian cancer tumor organoids (TOs). Each TO or source tissue associated with the TO (for example, a patient biopsy used to generate the TO) were genetically sequenced to determine whether the TO had variants (mutations) in homologous recombination proteins (including BRCA1 and BRCA2) and whether the TO was likely to have homologous recombination deficiency (HRD), according to an HRD engine.

None of the TOs had pathogenic single nucleotide variants (SNVs) in BRCA1 or BRCA2. One of the TOs had loss of heterozygosity (LOH) of BRCA1 or BRCA2 and had only one functioning copy of the gene. None of the TOs had bi-allelic loss of BRCA1 or BRCA2 (both a pathogenic SNV and LOH) and traditionally would not have been expected to have HRD or respond to PARPi therapy. BRCA mutation and LOH status was based on sequencing analysis of either the TO or the source tissue.

Regardless of the lack of bi-allelic BRCA loss, some of the TOs were analyzed by an HRD engine and predicted to have HRD based on other criteria.

The HRD engine is described in U.S. patent application Ser. No. 16/789,363, titled “An Integrated Machine-Learning Framework To Predict Homologous Recombination Deficiency”, filed Feb. 12, 2020, the contents of which are incorporated by reference herein in their entirety for any and all purposes. In another embodiment, the HRD score or likelihood of PARPi sensitivity may be determined by the trained classifier disclosed herein.

One of the TOs had a low HRD score (unlikely to have HRD or be sensitive to PARPi) and one of the TOs had a high HRD score (likely to have HRD and be sensitive to PARPi).

All of the TOs were grown in culture wells and each well was exposed for 96 hours to either a negative control (1% DMSO) or one of multiple PARPi therapies (Rucaparib, Niraparib, Pamiparib, Talazoparib, Olaparib, or Veliparib) at one of three concentrations (1 nM, 100 nM, or 10,000 nM). Some of the organoids were exposed to additional concentrations as noted in the x-axis of the figures.

At 96 hours the cells were stained by either caspase 3/7 or TO-PRO-3. Caspase 3/7 stained dying, apoptic cells and TO-PRO-3 stained dead cells. For each PARPi therapy, efficacy was measured at each concentration by detecting the proportion of viable cells that were not stained and normalizing that proportion to the proportion of viable cells in the negative control well, where the proportion of negative control well cells that were viable was adjusted to 100% or 75% (indicated in the figure). This normalization resulted in some experimental wells having a proportion of viable cells that was greater than 100% (or 75%). A best fit curve was generated for the viability proportion at each concentration and an inverse AUC was calculated as the area between actual cell viability (the best fit curve) and 100% (or 75%) cell viability. The inverse AUC served as an additional measure of PARPi efficacy, where a higher inverse AUC indicated a higher drug efficacy.

The PARPi therapies were hypothesized to be more effective against TOs with a high HRD score than TOs with a low HRD score.

The viability data shown below indicate that the PARPi therapies were more effective against TOs with a high HRD score than TOs with a low HRD score.

For organoids that were PARPi sensitive, PARPi therapies were effective against TOs that did not have BRCA1 or BRCA2 mutations or biallelic inactivation of BRCA1 or BRCA2.

FIGS. 14A and 14B illustrate viability data for a tumor organoid having a low HRD score, no BRCA1 or BRCA2 mutations, BRCA1 LOH, and no BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 15A and 15B illustrate viability data for a tumor organoid having a high HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control). Lower doses of PARPi were more effective for this organoid than the low HRD shown in the previous figures organoid.

Example 9 PARPi Sensitivity in Non-Small Cell Lung Cancer Cancer Tumor Organoids

In this example, PARPi sensitivity was measured for two non-small cell lung cancer tumor organoids (TOs). Each TO or source tissue associated with the TO (for example, a patient biopsy used to generate the TO) were genetically sequenced to determine whether the TO had variants (mutations) in homologous recombination proteins (including BRCA1 and BRCA2) and whether the TO was likely to have homologous recombination deficiency (HRD), according to an HRD engine.

None of the TOs had pathogenic single nucleotide variants (SNVs) in BRCA1 or BRCA2. None of the TOs had loss of heterozygosity (LOH) of BRCA1 or BRCA2. None of the TOs had bi-allelic loss of BRCA1 or BRCA2 (both a pathogenic SNV and LOH) and traditionally would not have been expected to have HRD or respond to PARPi therapy. BRCA mutation and LOH status was based on sequencing analysis of either the TO or the source tissue.

Regardless of the lack of bi-allelic BRCA loss, some of the TOs were analyzed by an HRD engine and predicted to have HRD based on other criteria.

The HRD engine is described in U.S. patent application Ser. No. 16/789,363, titled “An Integrated Machine-Learning Framework To Predict Homologous Recombination Deficiency”, filed Feb. 12, 2020, the contents of which are incorporated by reference herein in their entirety for any and all purposes. In another embodiment, the HRD score or likelihood of PARPi sensitivity may be determined by the trained classifier disclosed herein.

One of the TOs had a low HRD score (unlikely to have HRD or be sensitive to PARPi) and one of the TOs had a high HRD score (likely to have HRD and be sensitive to PARPi).

All of the TOs were grown in culture wells and each well was exposed for 96 hours to either a negative control (1% DMSO) or one of multiple PARPi therapies (Rucaparib, Niraparib, Pamiparib, Talazoparib, Olaparib, or Veliparib) at one of three concentrations (1 nM, 100 nM, or 10,000 nM). Some of the organoids were exposed to additional concentrations as noted in the x-axis of the figures.

At 96 hours the cells were stained by either caspase 3/7 or TO-PRO-3. Caspase 3/7 stained dying, apoptic cells and TO-PRO-3 stained dead cells. For each PARPi therapy, efficacy was measured at each concentration by detecting the proportion of viable cells that were not stained and normalizing that proportion to the proportion of viable cells in the negative control well, where the proportion of negative control well cells that were viable was adjusted to 100% or 75% (indicated in the figure). This normalization resulted in some experimental wells having a proportion of viable cells that was greater than 100% (or 75%). A best fit curve was generated for the viability proportion at each concentration and an inverse AUC was calculated as the area between actual cell viability (the best fit curve) and 100% (or 75%) cell viability. The inverse AUC served as an additional measure of PARPi efficacy, where a higher inverse AUC indicated a higher drug efficacy.

The PARPi therapies were hypothesized to be more effective against TOs with a high HRD score than TOs with a low HRD score.

The viability data shown below indicate that the PARPi therapies were more effective against TOs with a high HRD score than TOs with a low HRD score.

For organoids that were PARPi sensitive, PARPi therapies were effective against TOs that did not have BRCA1 or BRCA2 mutations or biallelic inactivation of BRCA1 or BRCA2.

FIGS. 16A and 16B illustrate viability data for a tumor organoid having a low HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

FIGS. 17A and 17B illustrate viability data for a tumor organoid having a high HRD score, no BRCA1 or BRCA2 mutations, no BRCA1 LOH and having BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

Example 10 PARPi Sensitivity in Endometrial Tumor Organoids

In this example, PARPi sensitivity was measured for one endometrial tumor organoid (TOs). Each TO or source tissue associated with the TO (for example, a patient biopsy used to generate the TO) were genetically sequenced to determine whether the TO had variants (mutations) in homologous recombination proteins (including BRCA1 and BRCA2) and whether the TO was likely to have homologous recombination deficiency (HRD), according to an HRD engine.

None of the TOs had pathogenic single nucleotide variants (SNVs) in BRCA1 or BRCA2. None of the TOs had loss of heterozygosity (LOH) of BRCA1 or BRCA2. None of the TOs had bi-allelic loss of BRCA1 or BRCA2 (both a pathogenic SNV and LOH) and traditionally would not have been expected to have HRD or respond to PARPi therapy. BRCA mutation and LOH status was based on sequencing analysis of either the TO or the source tissue.

The TO was analyzed by an HRD engine and predicted not to have HRD.

The HRD engine is described in U.S. patent applicaiton Ser. No. 16/789,363, titled “An Integrated Machine-Learning Framework To Predict Homologous Recombination Deficiency”, filed Feb. 12, 2020, the contents of which are incorporated by reference herein in their entirety for any and all purposes. In another embodiment, the HRD score or likelihood of PARPi sensitivity may be determined by the trained classifier disclosed herein.

One of the TOs had a low HRD score (unlikely to have HRD or be sensitive to PARPi).

All of the TOs were grown in culture wells and each well was exposed for 96 hours to either a negative control (1% DMSO) or one of multiple PARPi therapies (Rucaparib, Niraparib, Pamiparib, Talazoparib, Olaparib, or Veliparib) at one of three concentrations (1 nM, 100 nM, or 10,000 nM). Some of the organoids were exposed to additional concentrations as noted in the x-axis of the figures.

At 96 hours the cells were stained by either caspase 3/7 or TO-PRO-3. Caspase 3/7 stained dying, apoptic cells and TO-PRO-3 stained dead cells. For each PARPi therapy, efficacy was measured at each concentration by detecting the proportion of viable cells that were not stained and normalizing that proportion to the proportion of viable cells in the negative control well, where the proportion of negative control well cells that were viable was adjusted to 100% or 75% (indicated in the figure). This normalization resulted in some experimental wells having a proportion of viable cells that was greater than 100% (or 75%). A best fit curve was generated for the viability proportion at each concentration and an inverse AUC was calculated as the area between actual cell viability (the best fit curve) and 100% (or 75%) cell viability. The inverse AUC served as an additional measure of PARPi efficacy, where a higher inverse AUC indicated a higher drug efficacy.

The viability data shown below indicate that the PARPi therapies were not effective against a TO with a low HRD score.

FIGS. 18A and 18B illustrate viability data for a tumor organoid having a low HRD score, no BRCA1 or BRCA2 mutations and no BRCA1 or BRCA2 LOH. The x-axis label indicates the PARP-i therapy and dose. The y-axis indicates the percent of cells in the well that were viable, normalized to the DMSO mock condition (negative control).

REFERENCES CITED AND ALTERNATIVE EMBODIMENTS

All references cited herein are incorporated herein by reference in their entirety and for all purposes to the same extent as if each individual publication or patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety for all purposes.

The present invention can be implemented as a computer program product that comprises a computer program mechanism embedded in a non-transitory computer readable storage medium. For instance, the computer program product could contain the program modules shown in any combination in FIG. 1 and/or as described elsewhere within the application. These program modules can be stored on a CD-ROM, DVD, magnetic disk storage product, USB key, or any other non-transitory computer readable data or program storage product.

The methods and systems described above may be utilized in combination with or as part of a digital and laboratory health care platform that is generally targeted to medical care and research. It should be understood that many uses of the methods and systems described above, in combination with such a platform, are possible. One example of such a platform is described in U.S. patent application Ser. No. 16/657,804, titled “Data Based Cancer Research and Treatment Systems and Methods”, and filed Oct. 18, 2019, which is incorporated herein by reference and in its entirety for all purposes.

Many modifications and variations of this disclosure can be made without departing from its spirit and scope, as will be apparent to those skilled in the art. The specific embodiments described herein are offered by way of example only. The embodiments were chosen and described in order to best explain the principles of the invention and its practical applications, to thereby enable others skilled in the art to best utilize the invention and various embodiments with various modifications as are suited to the particular use contemplated. The disclosure is to be limited only by the terms of the appended claims, along with the full scope of equivalents to which such claims are entitled. 

1-8. (canceled)
 9. A method for training a classifier to discriminate between two or more tumor sensitivities to a poly ADP ribose polymerase (PARP) inhibitor, the method comprising: (A) obtaining, for each respective tissue sample in a plurality of tissue samples, a corresponding plurality of nucleic acid features of the respective tissue sample; (B) obtaining, for each respective tissue sample in the plurality of tissue samples, a corresponding indication of the sensitivity of a respective one or more organoids cultured from one or more cells of the respective tissue sample to the PARP inhibitor; and at a computer system comprising at least one processor and a memory storing at least one program for execution by the at least one processor: (C) training an untrained classifier against at least (i) the corresponding plurality of nucleic acid features and (ii) the corresponding indication of the sensitivity of the respective one or more organoids to the PARP inhibitor, across the plurality of tissue samples, thereby obtaining a trained classifier that discriminates between the two or more tumor sensitivities to the PARP inhibitor wherein a first tumor sensitivity in the two or more tumor sensitivities to the PARP inhibitor is associated with an indication of resistance to the PARP inhibitor, and a second tumor sensitivity in the two or more tumor sensitivities to the PARP inhibitor is associated with an indication of absence of resistance to the PARP inhibitor. 10-11. (canceled)
 12. The method of claim 9, wherein the PARP inhibitor is selected from the group consisting of olaparib, veliparib, rucaparib, niraparib, and talazoparib.
 13. The method of claim 9, wherein the classifier is further trained to discriminate between the two or more tumor sensitivities to the PARP inhibitor and one or more tumor sensitivities to a chemotherapeutic drug that is not a PARP inhibitor.
 14. (canceled)
 15. The method of claim 9, wherein each tissue sample in the plurality of tissue samples comprises a breast cancer biopsy.
 16. The method of claim 9, wherein each tissue sample in the plurality of tissue samples comprises an ovarian cancer biopsy.
 17. The method of claim 9, wherein each tissue sample in the plurality of tissue samples comprises a biopsy of a homologous recombination deficient (HRD) cancer.
 18. The method of claim 9, wherein each tissue sample in the plurality of tissue samples comprises a biopsy from a cancer other than breast cancer or ovarian cancer.
 19. The method of claim 9, wherein the plurality of nucleic acid features of the tissue sample comprises one or more of an indication of a presence of a single nucleotide variant at a genomic location, a methylation status at a genomic location, a relative copy number for a genomic location, an allelic ratio for a genomic location, a relative expression level of a gene, and mathematical combinations thereof.
 20. The method of claim 19, wherein the plurality of nucleic acid features of the tissue sample comprises a BRCA1 or BRCA2 mutant allele status.
 21. The method of claim 9, wherein at least a sub-plurality of the plurality of nucleic acid features of the respective tissue sample are measured from the respective one or more organoids cultured from one or more cells of the respective tissue sample.
 22. The method of claim 9, wherein the indication of the sensitivity of the respective one or more organoids to the PARP inhibitor is based at least in part on one or more cellular fitness measurements obtained by: i) exposing the respective one or more organoids to one or more amounts of the PARP inhibitor; and measuring the fitness of cells in the respective one or more organoids following the exposure to the one or more amounts of the PARP inhibitor, thereby obtaining the one or more cellular fitness measurements.
 23. The method of claim 22, wherein the one or more cellular fitness measurements are one or more measurements of cellular apoptosis following exposure to the one or more amounts of the PARP inhibitor.
 24. The method of claim 23, wherein, for at least one respective tissue sample in the plurality of tissue samples, the respective one or more organoids are exposed to a sensitizing therapy before being exposed to the PARP inhibitor.
 25. The method of claim 9, wherein the untrained classifier is further trained against, for each respective tissue sample in the plurality of tissue samples, (iii) a corresponding cancer classification of the tissue sample in a plurality of cancer classifications.
 26. The method of claim 25, wherein the plurality of cancer classifications comprises cancerous tissue and non-cancerous tissue.
 27. The method of claim 25, wherein the plurality of cancer classifications comprises a plurality of types of cancer.
 28. The method of claim 25, wherein the plurality of cancer classifications comprises a plurality of stages of a cancer.
 29. The method of claim 9, wherein: the plurality of tissue samples comprises a plurality of tumor biopsies; and the training (C) comprises identifying a plurality of genes that are differentially expressed between (i) organoids, cultured from one or more cells of a respective tumor biopsy in the plurality of tumor biopsies, that have the first tumor sensitivity to the PARP inhibitor, and (ii) organoids, cultured from one or more cells of a respective tumor biopsy in the plurality of tumor biopsies, that have the second tumor sensitivity to the PARP inhibitor.
 30. The method of claim 9, wherein the untrained classifier is further trained against, for each respective tissue sample in the plurality of tissue samples, (iv) one or more phenotypic characteristics of the respective tissue sample.
 31. The method of claim 30, wherein the one or more phenotypic characteristics of the tissue sample comprise a histologic feature of the tissue sample.
 32. The method of claim 9, wherein the untrained classifier is further trained against, for each respective tissue sample in the plurality of tissue samples, (v) one or more characteristics of the subject from which the tissue sample was obtained.
 33. The method of claim 9, wherein the classifier is a multinomial classifier that is trained to provide a plurality of likelihoods, wherein each respective likelihood in the plurality of likelihoods is a likelihood that tumor cells from a test subject with cancer will have a different respective sensitivity in the two or more tumor sensitivities to a PARP inhibitor.
 34. The method of claim 9, wherein the trained classifier is a neural network algorithm, a support vector machine algorithm, a Naive Bayes algorithm, a nearest neighbor algorithm, a boosted trees algorithm, a random forest algorithm, a convolutional neural network algorithm, a decision tree algorithm, a regression algorithm, or a clustering algorithm. 35-161. (canceled) 